[ { "id": "htan-wustl", "label": "HTAN WUSTL (Mo et al. 2024)", "citation": { "authors": "Mo CK, et al.", "title": "Tumour evolution and microenvironment interactions in 2D and 3D space", "journal": "Nature", "year": 2024, "doi": "10.1038/s41586-024-08087-4", "url": "https://doi.org/10.1038/s41586-024-08087-4" }, "related_citations": [ { "authors": "Iglesia MD, et al.", "title": "Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages", "journal": "Nature Cancer", "year": 2024, "doi": "10.1038/s43018-024-00773-6", "url": "https://doi.org/10.1038/s43018-024-00773-6" } ], "cancers": [ "BRCA", "COAD", "READ", "PDAC" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "he-original", "spatial-rna", "raw-reads" ], "techniques": [ "Visium", "Visium FFPE" ], "preservation": [ "Fresh frozen", "FFPE" ], "specimen": "clinical-tumour", "linkage": "same-section", "access": { "category": "account", "route": "Original H&E TIFFs, count matrices, coordinates and scale factors are open on Synapse after free registration. Raw reads are controlled through dbGaP (phs002371).", "links": [ [ "HTAN data portal", "https://data.humantumoratlas.org/" ], [ "dbGaP phs002371", "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002371.v1.p1" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": "Multi-cancer atlas from the Washington University HTAN centre. Breast, colorectal and pancreatic Visium captures are linked to patient-level clinical tables. Most colorectal captures are from metastases, and several breast captures were taken after neoadjuvant therapy; both groups are listed and labelled, not removed.", "notes": [ "H&E was imaged on the Visium section before library preparation (study methods). Image calibration and the full-resolution-to-spot transform have not been re-derived here.", "Breast clinical annotation follows the Iglesia et al. supplement where portal coding and the clinical table disagree.", "Pancreatic histology labels include pancreatobiliary-type and mixed carcinomas; these are not merged with conventional PDAC." ], "compartments": [ "primary-tumour", "metastatic-tumour" ], "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "janesick-2023", "label": "Janesick et al. 2023", "citation": { "authors": "Janesick A, et al.", "title": "High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis", "journal": "Nature Communications", "year": 2023, "doi": "10.1038/s41467-023-43458-x", "url": "https://doi.org/10.1038/s41467-023-43458-x" }, "cancers": [ "BRCA" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "he-original", "spatial-rna", "single-cell-rna", "raw-reads" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "same-section", "access": { "category": "open", "route": "Original H&E TIFF, counts and spatial bundle on GEO; raw reads on SRA.", "links": [ [ "GEO GSE243275", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243275" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": "A single primary invasive ductal carcinoma biopsy profiled with Visium CytAssist, Xenium and single-cell RNA. One deposited Visium capture is catalogued.", "notes": [ "The biopsy contains DCIS; invasive tumour regions need to be masked for an invasive-carcinoma analysis.", "Embedded and crosswalk image-resolution values disagree and have not been resolved.", "Treatment before biopsy is not reported." ], "compartments": [ "primary-tumour" ], "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "valdeolivas-2024", "label": "Valdeolivas et al. 2024", "citation": { "authors": "Valdeolivas A, et al.", "title": "Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics", "journal": "npj Precision Oncology", "year": 2024, "doi": "10.1038/s41698-023-00488-4", "url": "https://doi.org/10.1038/s41698-023-00488-4" }, "cancers": [ "COAD", "READ" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "he-original", "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "same-section-mapping-pending", "access": { "category": "open", "route": "Processed section archives and original NanoZoomer slide scans on Zenodo (CC BY 4.0).", "links": [ [ "Zenodo 7760264", "https://zenodo.org/records/7760264" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": "Seven colorectal cancer patients with two Visium sections each. The original slide scans cover whole glass slides, so each capture area still has to be located on its scan.", "notes": [ "All retained tumour donors had no pretreatment according to the publication's patient table.", "One donor has mucinous adenocarcinoma and is kept outside the conventional stratum; one donor's sections are predominantly non-neoplastic and are excluded; one capture has author-reported low RNA quality.", "Some primary tumours come from patients with liver or lymph-node metastases." ], "compartments": [ "primary-tumour" ], "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "oliveira-2025", "label": "Oliveira et al. 2025 (Visium HD)", "citation": { "authors": "Oliveira MFd, et al.", "title": "High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer", "journal": "Nature Genetics", "year": 2025, "doi": "10.1038/s41588-025-02193-3", "url": "https://doi.org/10.1038/s41588-025-02193-3" }, "cancers": [ "COAD", "READ" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "he-original", "spatial-rna", "raw-reads" ], "techniques": [ "Visium HD" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "same-section", "access": { "category": "open", "route": "Original BigTIFF H&E, 8 µm binned matrices, positions and alignment files on GEO; raw reads on SRA.", "links": [ [ "GEO GSE280318", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE280318" ] ] }, "verification": "file-checked", "verified_on": "2026-10-09", "description": "Visium HD profiles of colorectal tumours with same-section high-resolution H&E. Three tumour sections are catalogued; normal-adjacent sections are excluded.", "notes": [ "Primary versus metastatic specimen status is not stated explicitly; these captures are listed as under review.", "The publication reports the patients as pretreatment." ], "compartments": [ "tumour-unspecified" ], "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "zhang-2024-thca", "label": "Zhang et al. 2024 (thyroid)", "citation": { "authors": "Zhang X, et al.", "title": "CD36+ Proinflammatory Macrophages Interact with ZCCHC12+ Tumor Cells in Papillary Thyroid Cancer Promoting Tumor Progression and Recurrence", "journal": "Cancer Immunology Research", "year": 2024, "doi": "10.1158/2326-6066.CIR-23-1047", "url": "https://doi.org/10.1158/2326-6066.CIR-23-1047" }, "cancers": [ "THCA" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "he-original", "spatial-rna", "raw-reads" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "same-section", "access": { "category": "open", "route": "Counts, coordinates and original-resolution JPEG H&E on GEO; raw reads on SRA.", "links": [ [ "GEO GSE230424", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230424" ] ] }, "verification": "file-checked", "verified_on": "2026-10-09", "description": "Two primary papillary thyroid carcinomas with Hashimoto thyroiditis in the background.", "notes": [ "Papillary carcinoma variant and treatment history are not reported.", "Two further GEO samples in the series are thyroiditis-only tissue and are not tumour captures." ], "compartments": [ "primary-tumour" ], "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "gouin-2021", "label": "Gouin et al. 2021", "citation": { "authors": "Gouin KH, et al.", "title": "An N-Cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer", "journal": "Nature Communications", "year": 2021, "doi": "10.1038/s41467-021-25103-7", "url": "https://doi.org/10.1038/s41467-021-25103-7" }, "cancers": [ "BLCA" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "he-original", "spatial-rna", "raw-reads" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "same-section", "access": { "category": "open", "route": "Original capture-area JPEGs, processed counts and coordinates on GEO; raw reads on SRA.", "links": [ [ "GEO GSE171351", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171351" ] ] }, "verification": "file-checked", "verified_on": "2026-10-09", "description": "Four treatment-naive patients with high-grade muscle-invasive urothelial carcinoma.", "notes": [ "The H&E images cover the capture area rather than the whole resection slide.", "Detailed variant morphology is not reported and would need pathology review.", "Two image-scale estimates differ (about 0.41 and 0.49 µm/pixel)." ], "compartments": [ "primary-tumour" ], "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "gse245908-lihc", "label": "Giraud et al. 2024", "citation": { "authors": "Giraud J, et al.", "title": "THBS1+ myeloid cells expand in SLD hepatocellular carcinoma and contribute to immunosuppression and unfavorable prognosis through TREM1", "journal": "Cell Reports", "year": 2024, "doi": "10.1016/j.celrep.2024.113773", "url": "https://doi.org/10.1016/j.celrep.2024.113773" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "he-original", "spatial-rna", "raw-reads" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "same-section", "access": { "category": "open", "route": "Processed counts, coordinates, original TIFF and raw reads on GEO/SRA without registration.", "links": [ [ "GEO GSE245908", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245908" ] ] }, "verification": "file-checked", "verified_on": "2026-10-09", "description": "Two untreated hepatocellular carcinoma resections.", "notes": [ "Original H&E files are attached to a different GSM record than their expression data; the series' own mapping table resolves this.", "TIFF calibration and the spot-based estimate differ (about 0.45 and 0.38 µm/pixel)." ], "compartments": [ "primary-tumour" ], "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "steiner-2026", "label": "Steiner et al. 2026", "citation": { "authors": "Steiner D, et al.", "title": "Vascular invasion-associated gene expression is detectable in pre-surgical biopsies of stage I lung adenocarcinoma", "journal": "Nature Communications", "year": 2026, "doi": "10.1038/s41467-026-70600-2", "url": "https://doi.org/10.1038/s41467-026-70600-2" }, "cancers": [ "LUAD" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "he-original", "spatial-rna", "raw-reads" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "same-section", "access": { "category": "open", "route": "Counts, coordinates and spot pathology labels on GEO; original whole-slide TIFFs on Zenodo; raw reads on SRA.", "links": [ [ "GEO GSE273378", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE273378" ], [ "Zenodo 21842070 (original scans)", "https://zenodo.org/records/21842070" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": "Thirteen untreated patients with resected stage I invasive non-mucinous lung adenocarcinoma. Two patients contributed two captures each.", "notes": [ "One capture that failed tissue-detachment QC in the study is excluded.", "Some original scans are supplied in flipped orientation by the authors; check orientation against coordinates." ], "compartments": [ "primary-tumour" ], "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "simkin-2026", "label": "Simkin et al. 2026", "citation": { "authors": "Simkin D, et al.", "title": "Spatial analysis of head and neck cancer identifies two ecosystems with distinct modes of epithelial-to-mesenchymal transition", "journal": "Nature Genetics", "year": 2026, "doi": "10.1038/s41588-026-02723-7", "url": "https://doi.org/10.1038/s41588-026-02723-7" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "he-original", "spatial-rna", "raw-reads" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "same-section", "access": { "category": "open", "route": "Native TIFF H&E, count matrices, coordinates and scale factors on GEO; raw reads via BioProject PRJNA1114040.", "links": [ [ "GEO GSE268014", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE268014" ] ] }, "verification": "file-checked", "verified_on": "2026-10-09", "description": "Twenty primary head and neck squamous cell carcinomas: twelve HPV-negative keratinizing and eight HPV-positive nonkeratinizing.", "notes": [ "The clinical table records prior treatment as NA for eighteen patients without defining NA; these are catalogued as unknown, not untreated.", "One patient had prior radiation and one documented second primary had earlier surgery and chemoradiation.", "Additional Visium HD sections from the same study are listed separately as candidates." ], "compartments": [ "primary-tumour" ], "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "pei-2025", "label": "Pei et al. 2025", "citation": { "authors": "Pei G, et al.", "title": "Spatial mapping of transcriptomic plasticity in metastatic pancreatic cancer", "journal": "Nature", "year": 2025, "doi": "10.1038/s41586-025-08927-x", "url": "https://doi.org/10.1038/s41586-025-08927-x" }, "cancers": [ "PDAC" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "he-original", "spatial-rna", "raw-reads" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "same-section", "access": { "category": "open", "route": "Original H&E JPEGs, filtered matrices and spatial folders on GEO; raw reads on SRA.", "links": [ [ "GEO GSE274557", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE274557" ] ] }, "verification": "file-checked", "verified_on": "2026-10-09", "description": "Rapid-autopsy cohort of thirteen PDAC patients with Visium captures from primary tumours and metastatic sites. Primary-site captures come from end-stage disease, not early surgical resections.", "notes": [ "Five patients had no treatment before collection; eight were treated.", "Two patient-derived xenograft sections in the series are excluded.", "Two captures are held for low tumour content or low RNA depth, and two have lower image resolution (about 0.68 µm/pixel)." ], "compartments": [ "primary-tumour", "metastatic-tumour" ], "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "schmitt-2026", "label": "Schmitt et al. 2026", "citation": { "authors": "Schmitt AM, et al.", "title": "Spatially-resolved subtype progression reveals metabolic vulnerabilities in pancreatic ductal adenocarcinoma", "journal": "Molecular Cancer", "year": 2026, "doi": "10.1186/s12943-026-02628-3", "url": "https://doi.org/10.1186/s12943-026-02628-3" }, "cancers": [ "PDAC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "he-downsampled", "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "access": { "category": "open", "route": "Processed matrices, coordinates and scale factors on ArrayExpress; only downsampled H&E images are listed.", "links": [ [ "ArrayExpress E-MTAB-15702", "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15702" ] ] }, "reported": [ [ 14, "patients", "untreated primary resections, per the publication and SDRF" ] ], "verification": "file-checked", "verified_on": "2026-10-16", "description": "Fourteen untreated primary PDAC resections profiled with Visium FFPE. The original 40× scans have not been located, so the captures are not counted as matched packages.", "compartments": [ "primary-tumour" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "14 preview images; no original scan in complete deposited file listing", "molecular_finding": "14 barcode vectors match matrix headers/all array positions; explicit in-tissue filter", "next_step": "Original scans; clinical and image QC.", "sections_listed": 14, "study_local_donors": 14 }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "tcga-brca", "label": "TCGA-BRCA", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-BRCA" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "BRCA" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "BRCA", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-BRCA" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Breast invasive carcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "BRCA" }, { "id": "tcga-coad", "label": "TCGA-COAD", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-COAD" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "COAD", "CRC" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "COAD", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-COAD" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Colon adenocarcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Analysed with TCGA-READ as the pooled colorectal cohort (CRC). Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Analysed with TCGA-READ as the pooled colorectal cohort (CRC). COAD counts are provenance; two COAD-submitted rectal primaries are included in CRC.", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "CRC" }, { "id": "tcga-read", "label": "TCGA-READ", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-READ" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "READ", "CRC" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "READ", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-READ" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Rectal adenocarcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Below the molecular screen on its own and included through the pooled colorectal cohort (CRC) with TCGA-COAD. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Below the screen on its own (156 patients, 94 with both assays after assay QC); analysed with TCGA-COAD as the pooled colorectal cohort (CRC), which meets it.", "Two READ-submitted cases are annotated as colon primaries; they stay in CRC with both the reported site and the annotation override recorded.", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "CRC" }, { "id": "tcga-thca", "label": "TCGA-THCA", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-THCA" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "THCA" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "THCA", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-THCA" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Thyroid carcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "THCA" }, { "id": "tcga-blca", "label": "TCGA-BLCA", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-BLCA" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "BLCA" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "BLCA", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-BLCA" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Bladder urothelial carcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "BLCA" }, { "id": "tcga-lgg", "label": "TCGA-LGG", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-LGG" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "LGG", "GLIOMA" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "LGG", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour" ], "linkage": "same-patient", "gates": [ "integrated-diagnosis", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-LGG" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Lower-grade glioma. Slide images, RNA-seq and Illumina 450k methylation from the same patients. Analysed with TCGA-GBM as the pooled glioma classification benchmark (GLIOMA), not as a discovery cohort. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; integrated WHO diagnosis and grade have not been adjudicated.", "notes": [ "Contributes 502 patients, all with both assays, to the GLIOMA benchmark; the LGG-only subset is not counted as a separate cohort.", "Historical histology and grade, raw IDH and 1p/19q calls and the published molecular groups are kept as separate annotations.", "No solid normal tissue with retained RNA and a slide image is available." ], "analysis_cohort": "GLIOMA" }, { "id": "tcga-gbm", "label": "TCGA-GBM", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-GBM" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "GBM", "GLIOMA" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "GBM", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "integrated-diagnosis", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-GBM" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Glioblastoma, as historically diagnosed in TCGA. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from a few donors. Below the molecular screen on its own and included only through the pooled glioma classification benchmark (GLIOMA) with TCGA-LGG. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; integrated WHO diagnosis and grade have not been adjudicated.", "notes": [ "Below the screen on its own (242 patients, 51 with both assays after assay QC); 225 pass the patient screen, 46 with both assays.", "Many GBM RNA-seq aliquots have no exact match in the PanCanAtlas quality annotations and stay unresolved.", "The five normal packages come from normal-only donors without a reported primary diagnosis; they are not verified matched glioblastoma controls." ], "analysis_cohort": "GLIOMA" }, { "id": "tcga-lihc", "label": "TCGA-LIHC", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-LIHC" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "LIHC" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "LIHC", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-LIHC" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Liver hepatocellular carcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "LIHC" }, { "id": "tcga-luad", "label": "TCGA-LUAD", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-LUAD" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "LUAD" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "LUAD", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-LUAD" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Lung adenocarcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Pathology-group exclusions include unclassified non-small cell carcinoma and cases favouring large cell neuroendocrine carcinoma.", "GDC also lists EPIC v2 methylation for 53 primary LUAD patients; it is a different platform from 450k and is not counted.", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "LUAD" }, { "id": "tcga-hnsc", "label": "TCGA-HNSC", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-HNSC" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "HNSC" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "HNSC", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-HNSC" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Head and neck squamous cell carcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "HNSC" }, { "id": "tcga-paad", "label": "TCGA-PAAD", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-PAAD" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "PDAC" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "PAAD", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-PAAD" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Pancreatic adenocarcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked beyond the histology review.", "notes": [ "Pathology-group exclusions removed neuroendocrine and acinar tumours, intraductal papillary mucinous neoplasms, tumours of non-pancreatic origin and samples with very low neoplastic cellularity. The retained patients are still not a curated conventional PDAC series.", "A proposed confirmed PDAC cohort of 149 patients (143 with RNA-seq and 450k, six with 450k only) is defined by documented pathology review; see the PDAC page. It is one patient below the general 150-patient threshold.", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "PDAC" }, { "id": "cand-wu-2021", "label": "Wu et al. 2021", "title": "A single-cell and spatially resolved atlas of human breast cancers", "citation": { "authors": "Wu SZ, et al.", "title": "A single-cell and spatially resolved atlas of human breast cancers", "journal": "Nature Genetics", "year": 2021, "doi": "10.1038/s41588-021-00911-1", "url": "https://www.nature.com/articles/s41588-021-00911-1" }, "cancers": [ "BRCA" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "Zenodo 4739739", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41588-021-00911-1" ], [ "Data record", "https://zenodo.org/records/4739739" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "Six Space Ranger previews; large image PDF also inspected, no verified original scan/capture transform", "molecular_finding": "All six expression barcode sets join positions; two exactly match in-tissue sets. Four filtered matrices retain fewer spots, and three contain 6/2/2 out-of-tissue spots; explicit in-tissue filtering and no invented expression for omitted rows. Six patientid fields verified.", "next_step": "Original scans and the provenance of the image PDF; filter the out-of-tissue spots in three sections explicitly.", "sections_listed": 6, "study_local_donors": 6 }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-bassiouni-gse210616", "label": "Spatial transcriptomic analysis of a diverse patient cohort reveals a conserved architecture in triple-negative breast cancer", "title": "Spatial transcriptomic analysis of a diverse patient cohort reveals a conserved architecture in triple-negative breast cancer", "citation": { "authors": null, "title": "Spatial transcriptomic analysis of a diverse patient cohort reveals a conserved architecture in triple-negative breast cancer", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9812886/" }, "cancers": [ "BRCA" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE210616", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC9812886/" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210616" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "43 previews", "molecular_finding": "All 43 exact barcode/in-tissue agreements", "next_step": "Treatment, original scans and registration QC.", "sections_listed": 43, "study_local_donors": 22 }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-bcarc-tls-hev-2026", "label": "Spatial atlas of tertiary lymphoid structures and high endothelial venules in breast cancer", "title": "Spatial atlas of tertiary lymphoid structures and high endothelial venules in breast cancer", "citation": { "authors": null, "title": "Spatial atlas of tertiary lymphoid structures and high endothelial venules in breast cancer", "journal": null, "year": null, "doi": null, "url": null }, "cancers": [ "BRCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium HD" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "not-released" ], "accession": "Zenodo 18917100; S-BIAD3080; EGAD00001016794", "access": { "category": "unreleased", "route": null, "links": [ [ "Data record", "https://zenodo.org/records/18917100" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "release-gap", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Public record exists but lists no downloadable files", "molecular_finding": "No molecular package inspectable", "next_step": "Await an actionable public file release; do not count record views as released data.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Release search", "depth": "bounded Europe PMC title search", "result": "A bounded literature search found no measured spatial package with original images; other routes may still need review." } ] } }, { "id": "cand-official-10x-breast-demos", "label": "10x Genomics human breast Visium demonstration datasets", "title": "10x Genomics human breast Visium demonstration datasets", "citation": { "authors": null, "title": "10x Genomics human breast Visium demonstration datasets", "journal": null, "year": null, "doi": null, "url": null }, "cancers": [ "BRCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium HD", "Visium CytAssist" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "package-unverified", "identity" ], "accession": "Official dataset pages; HEST TENX13/14/23/24/39/53/68", "access": { "category": "open", "route": null, "links": [ [ "Data record", "https://www.10xgenomics.com/datasets" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "unspecified-vendor-lead", "depth": "source or metadata only", "states": [ "vendor-terms" ], "image_finding": "Generic vendor catalogue, no pinned specimen/version", "molecular_finding": "No uniquely identified package", "next_step": "Pin exact dataset, specimen, assay and version; respect vendor registration/terms; deduplicate other breast entries.", "sections_listed": null, "study_local_donors": null } }, { "id": "cand-wang-venet-2024-legacy-st", "label": "Wang et al. 2024", "title": "Spatial transcriptomics reveals substantial heterogeneity in triple-negative breast cancer with potential clinical implications", "citation": { "authors": "Wang X, et al.", "title": "Spatial transcriptomics reveals substantial heterogeneity in triple-negative breast cancer with potential clinical implications", "journal": "Nature Communications", "year": 2024, "doi": "10.1038/s41467-024-54145-w", "url": "https://www.nature.com/articles/s41467-024-54145-w" }, "cancers": [ "BRCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Spatial Transcriptomics (legacy arrays)" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "platform", "package-unverified" ], "accession": "Zenodo 13867935", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41467-024-54145-w" ], [ "Code (Zenodo 13867935)", "https://zenodo.org/records/13867935" ], [ "Data record (Zenodo 8135721)", "https://zenodo.org/records/8135721" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "public listing or archive inventoried", "states": [ "public-download", "local-qc" ], "image_finding": "Original image archive located, 25.3 GB; older catalogue link is code, not assay data", "molecular_finding": "Primary paper gives distinct public data record 8135721 with counts, clinical and array archives", "next_step": "Use 8135721, inspect code/data README and array-to-patient/image join; old 13867935/36 is code.", "sections_listed": null, "study_local_donors": null }, "reported": [ [ 281, "arrays", "Zenodo 8135721 clinical archive" ], [ 94, "clinical IDs", "Zenodo 8135721 clinical archive" ] ], "followup_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "complete README and 64 KB clinical archive; base-R object join", "findings": "The complete README and clinical archive join 281 arrays to 94 clinical IDs; the count, coordinate and original-image association is not yet verified.", "next_step": "Inspect selected array and image members and verify the count, coordinate and image join, keeping arrays and donors separate.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-dartmouth-aacr2026-1442", "label": "TNBC spatial transcriptomics resource (AACR 2026 abstract 1442)", "title": "TNBC spatial transcriptomics resource (AACR 2026 abstract 1442)", "citation": { "authors": null, "title": "TNBC spatial transcriptomics resource (AACR 2026 abstract 1442)", "journal": null, "year": null, "doi": null, "url": null }, "cancers": [ "BRCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "not-released" ], "accession": null, "access": { "category": "unreleased", "route": null, "links": [] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "release-unresolved", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Official AACR2026 abstract reports matched 40x H&E/Visium for 25 TNBC patients; no accession/reusable package identified", "molecular_finding": "Source-described measured Visium, not a downloaded matrix/coordinate package", "next_step": "Find final publication and released accession, then inspect patient/section/image files; 25 is a reported denominator, not available matched patients.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Release search", "depth": "bounded Europe PMC title search", "result": "A bounded literature search found no measured spatial package with original images; other routes may still need review." } ] } }, { "id": "cand-crc-colonmap-heiser2023", "label": "Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors", "title": "Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors", "citation": { "authors": null, "title": "Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10756562/" }, "cancers": [ "COAD", "READ" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "pathology-review" ], "accession": "HTAN Vanderbilt / Colon Molecular Atlas Project; OSF hftq2", "access": { "category": "account", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10756562/" ], [ "Data record", "https://data.humantumoratlas.org/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "account-route", "depth": "source or metadata only", "states": [ "account-registration" ], "image_finding": "HTAN public manifest behind a free account", "molecular_finding": "No newly downloaded package in this pass", "next_step": "Pin Vanderbilt/COLON MAP section/file IDs, donor and histology crosswalk; separate from WUSTL and cottam reuse.", "sections_listed": null, "study_local_donors": null } }, { "id": "cand-crc-orgares-gse283052", "label": "Neve et al. 2026", "title": "OrgaRES colorectal Visium resource", "citation": { "authors": "Neve B, et al.", "title": "Long non-coding RNA UCA1 modulates SMARCA2-containing SWI/SNF chromatin remodeling complexes in human colorectal cancer", "journal": "iScience", "year": 2026, "doi": "10.1016/j.isci.2025.114283", "url": "https://doi.org/10.1016/j.isci.2025.114283" }, "cancers": [ "COAD", "READ" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE283052", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://doi.org/10.1016/j.isci.2025.114283" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE283052" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "12 previews", "molecular_finding": "Shared series barcode vector matches all 4,992 positions in each of 12 matrices; in-tissue filtering required", "next_step": "Map donor IDs and primary or metastatic site before counting patients; keep the shared barcode-vector provenance.", "sections_listed": 12, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-crc-mahidol-gse267401", "label": "Primary colorectal cancer and liver metastasis, Visium CytAssist", "title": "Primary colorectal cancer and liver metastasis, Visium CytAssist", "citation": { "authors": null, "title": "Primary colorectal cancer and liver metastasis, Visium CytAssist", "journal": null, "year": null, "doi": null, "url": "https://pubmed.ncbi.nlm.nih.gov/39499374/" }, "cancers": [ "COAD", "READ" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE267401", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pubmed.ncbi.nlm.nih.gov/39499374/" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE267401" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "Four previews", "molecular_finding": "All unfiltered expression barcodes have positions; select in-tissue rows explicitly", "next_step": "Original scans and treatment; the primary and metastatic sections of patients 21 and 17 stay separate sites.", "sections_listed": 4, "study_local_donors": 2 }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-crc-miso-petacc8", "label": "Schmauch et al. 2025", "title": "MISO / PETACC-8 stage III colon adenocarcinoma Visium study", "citation": { "authors": "Schmauch B, et al.", "title": "A deep learning-based multiscale integration of spatial omics with tumor morphology", "journal": "Nature Communications", "year": 2025, "doi": "10.1038/s41467-025-66691-y", "url": "https://www.nature.com/articles/s41467-025-66691-y" }, "cancers": [ "COAD", "READ" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled", "identity" ], "accession": null, "access": { "category": "controlled", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41467-025-66691-y" ], [ "Data record", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12748640/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "access-dependent", "depth": "access boundary reached", "states": [ "dac-approval" ], "image_finding": "Primary paper retrieved; no controlled files accessed", "molecular_finding": "Package not available within approved scope", "next_step": "FFCD controls measured PETACC8-Visium use; separate measured packages from model-predicted outputs, and verify any public processed alternative before a permission decision.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-crc-vri-dartmouth2025", "label": "Srinivasan et al. 2025", "title": "Histology-Based Virtual RNA Inference Identifies Pathways Associated With Metastasis Risk in Colorectal Cancer", "citation": { "authors": "Srinivasan G, et al.", "title": "Histology-Based Virtual RNA Inference Identifies Pathways Associated With Metastasis Risk in Colorectal Cancer", "journal": "Modern Pathology", "year": 2025, "doi": "10.1016/j.modpat.2025.100866", "url": "https://doi.org/10.1016/j.modpat.2025.100866" }, "cancers": [ "COAD", "READ" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Spatial Transcriptomics (legacy arrays)", "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "release-unresolved" ], "accession": null, "access": { "category": "unresolved", "route": null, "links": [ [ "Publication", "https://doi.org/10.1016/j.modpat.2025.100866" ], [ "Data record", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12045403/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "release-unresolved", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Primary paper confirms measured Visium development cohort; predicted validation outputs are a different modality", "molecular_finding": "No actionable measured package verified", "next_step": "Locate released measured development-cohort files; do not count virtual RNA as measured spatial RNA.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Release search", "depth": "bounded Europe PMC title search", "result": "A bounded literature search found no measured spatial package with original images; other routes may still need review." }, { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-crc-liu-maru2026", "label": "Liu et al. 2026", "title": "Paired colorectal primary, liver and lung metastasis spatial atlas", "citation": { "authors": "Liu Y, et al.", "title": "Spatial multi-omics landscape of colorectal cancer macro- and micrometastases", "journal": "Cancer Cell", "year": 2026, "doi": "10.1016/j.ccell.2026.06.009", "url": "https://doi.org/10.1016/j.ccell.2026.06.009" }, "cancers": [ "COAD", "READ" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium HD" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "pathology-review", "image-qc", "calibration" ], "accession": "GSE294385; Zenodo 19043057", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://doi.org/10.1016/j.ccell.2026.06.009" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294385" ], [ "Further processed data (Zenodo 19043057; no files listed)", "https://zenodo.org/records/19043057" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "37 previews", "molecular_finding": "All 37 archive packages exact", "next_step": "Donor count and treatment; all 37 tissues are colorectal metastases.", "sections_listed": 37, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "outcome": "preview-additional-route", "depth": "primary data-availability statement and linked Zenodo record metadata", "findings": "The paper links further processed data in Zenodo 19043057, but the record listed no downloadable files when checked; the 37 Visium records are unchanged.", "next_step": "Check Zenodo 19043057 for a file release and a clinical sample join; no records are added from it yet.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-crc-spatch-ren2025", "label": "Ren et al. 2025", "title": "Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors (colorectal sample)", "citation": { "authors": "Ren P, et al.", "title": "Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors", "journal": "Nature Communications", "year": 2025, "doi": "10.1038/s41467-025-64292-3", "url": "https://www.nature.com/articles/s41467-025-64292-3" }, "cancers": [ "COAD", "READ" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium HD" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "pathology-review", "package-unverified" ], "accession": "S-BIAD1900; GSA HRA011129", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41467-025-64292-3" ], [ "Images (BioImage Archive S-BIAD1900)", "https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1900" ], [ "Code (Zenodo 16992659)", "https://zenodo.org/records/16992659" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "public listing or archive inventoried", "states": [ "public-download", "local-qc" ], "image_finding": "Original HE/CODEX/DAPI listings in S-BIAD1900, across five assays", "molecular_finding": "RNA count/coordinate package not yet joined; Zenodo 16992659 is code", "next_step": "Match each COAD platform to its measured RNA/coordinates; do not count CODEX/DAPI as H&E or colon specimens as READ.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Package join", "depth": "public file-list metadata", "result": "The public 36-file image list does not establish which RNA and coordinates belong to each COAD platform." } ] } }, { "id": "cand-crc-cottam-htan2025", "label": "HTAN Vanderbilt colorectal CytAssist captures", "title": "HTAN Vanderbilt colorectal CytAssist captures", "citation": { "authors": null, "title": "HTAN Vanderbilt colorectal CytAssist captures", "journal": null, "year": null, "doi": null, "url": null }, "cancers": [ "COAD", "READ" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "pathology-review", "identity" ], "accession": "HTAN Vanderbilt syn64759085/86/59111/59112; h5ad syn64759245/46", "access": { "category": "account", "route": null, "links": [ [ "Data record", "https://data.humantumoratlas.org/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "account-route", "depth": "source or metadata only", "states": [ "account-registration" ], "image_finding": "HTAN public portal behind a free account", "molecular_finding": "No newly inspected package", "next_step": "Pin exact study/HTAN donor-capture manifest and deduplicate Heiser/COLON MAP/WUSTL; preserve primary/metastatic labels.", "sections_listed": null, "study_local_donors": null } }, { "id": "cand-liao-2025-gse250521", "label": "Liao et al. 2025", "title": "A spatially resolved transcriptome landscape during thyroid cancer progression", "citation": { "authors": "Liao T, et al.", "title": "A spatially resolved transcriptome landscape during thyroid cancer progression", "journal": "Cell Reports Medicine", "year": 2025, "doi": "10.1016/j.xcrm.2025.102043", "url": "https://doi.org/10.1016/j.xcrm.2025.102043" }, "cancers": [ "THCA" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE250521", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://doi.org/10.1016/j.xcrm.2025.102043" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE250521" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "16 checked Visium previews; four ATC sections outside selected histology", "molecular_finding": "All 16 Visium packages exact; nine scRNA samples excluded from spatial counts", "next_step": "Original scans; four anaplastic thyroid carcinoma sections and nine single-cell samples stay outside this selection.", "sections_listed": 12, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-loberg-2026-jci191990", "label": "An integrated single-cell and spatial transcriptomic atlas of thyroid cancer progression identifies prognostic fibroblast subpopulations", "title": "An integrated single-cell and spatial transcriptomic atlas of thyroid cancer progression identifies prognostic fibroblast subpopulations", "citation": { "authors": null, "title": "An integrated single-cell and spatial transcriptomic atlas of thyroid cancer progression identifies prognostic fibroblast subpopulations", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12890526/" }, "cancers": [ "THCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "request" ], "accession": null, "access": { "category": "request", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12890526/" ], [ "Data record", "https://github.com/mloberg16/THCA_Fibroblast_Atlas" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "access-dependent", "depth": "access boundary reached", "states": [ "author-release" ], "image_finding": "Article explicitly restricts individual spatial data under IRB policy", "molecular_finding": "No individual package public", "next_step": "Lead-contact/institutional permission required for individual data; aggregate results on request do not replace spatial package.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "primary availability XML read", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-yan-2024-hra003537", "label": "Spatial transcriptomics reveals prognosis-associated cellular heterogeneity in the papillary thyroid carcinoma microenvironment", "title": "Spatial transcriptomics reveals prognosis-associated cellular heterogeneity in the papillary thyroid carcinoma microenvironment", "citation": { "authors": null, "title": "Spatial transcriptomics reveals prognosis-associated cellular heterogeneity in the papillary thyroid carcinoma microenvironment", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10905537/" }, "cancers": [ "THCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled", "serial-section" ], "accession": "HRA003537 / PRJCA013525", "access": { "category": "controlled", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10905537/" ], [ "Data record", "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA003537" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "access-dependent", "depth": "access boundary reached", "states": [ "dac-approval" ], "image_finding": "Primary paper and public code found; raw HRA route", "molecular_finding": "No matched processed original-image package inspected", "next_step": "Locate processed public supplement/image package independently of controlled raw reads.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "primary availability XML read", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-zhang-2025-prjca021247", "label": "Single-cell RNA-sequencing and spatial transcriptomic analysis reveal a distinct population of APOE-negative cells yielding pathological lymph node metastasis in papillary thyroid cancer", "title": "Single-cell RNA-sequencing and spatial transcriptomic analysis reveal a distinct population of APOE-negative cells yielding pathological lymph node metastasis in papillary thyroid cancer", "citation": { "authors": null, "title": "Single-cell RNA-sequencing and spatial transcriptomic analysis reveal a distinct population of APOE-negative cells yielding pathological lymph node metastasis in papillary thyroid cancer", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11733439/" }, "cancers": [ "THCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "release-unresolved" ], "accession": "PRJCA021247", "access": { "category": "unresolved", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11733439/" ], [ "Data record", "https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA021247" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "release-unresolved", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Primary paper identifies PRJCA021247 for scRNA/ST", "molecular_finding": "Public processed image package unverified", "next_step": "Resolve project-to-spatial accession and processed original-image/coordinate release.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Release search", "depth": "bounded Europe PMC title search", "result": "A bounded literature search found no measured spatial package with original images; other routes may still need review." }, { "check": "Public processed alternative", "depth": "primary availability XML read", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-wang-2024-hra005594", "label": "Interactions between LAMP3+ dendritic cells and T-cell subpopulations promote immune evasion in papillary thyroid carcinoma", "title": "Interactions between LAMP3+ dendritic cells and T-cell subpopulations promote immune evasion in papillary thyroid carcinoma", "citation": { "authors": null, "title": "Interactions between LAMP3+ dendritic cells and T-cell subpopulations promote immune evasion in papillary thyroid carcinoma", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11141193/" }, "cancers": [ "THCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "request" ], "accession": "HRA005594", "access": { "category": "request", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11141193/" ], [ "Data record", "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA005594" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "author-release", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Primary article says data on reasonable request; HRA raw route separate", "molecular_finding": "No public matched package", "next_step": "Author/repository release of processed matrix, coordinates and original image.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "primary availability XML read", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-seok-2025-cii", "label": "Tumor microenvironment remodeling across thyroid cancer differentiation states revealed by spatial transcriptomics", "title": "Tumor microenvironment remodeling across thyroid cancer differentiation states revealed by spatial transcriptomics", "citation": { "authors": null, "title": "Tumor microenvironment remodeling across thyroid cancer differentiation states revealed by spatial transcriptomics", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12583360/" }, "cancers": [ "THCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "request" ], "accession": null, "access": { "category": "request", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12583360/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "author-release", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Primary full text retrieved; no reusable file package established", "molecular_finding": "Unverified", "next_step": "Locate a released processed-data accession or obtain author release later.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-li-2025-s12967-07566", "label": "Integrated spatial metabolomics and transcriptomics reveal the molecular landscape of papillary thyroid cancer and its lymph node metastasis", "title": "Integrated spatial metabolomics and transcriptomics reveal the molecular landscape of papillary thyroid cancer and its lymph node metastasis", "citation": { "authors": null, "title": "Integrated spatial metabolomics and transcriptomics reveal the molecular landscape of papillary thyroid cancer and its lymph node metastasis", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12821195/" }, "cancers": [ "THCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "request" ], "accession": null, "access": { "category": "request", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12821195/" ], [ "Data record", "https://metaspace2020.org/project/kening-2025" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "author-release", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Metaspace is released metabolomics, not spatial RNA", "molecular_finding": "Paper explicitly says spatial RNA not publicly deposited", "next_step": "Processed spatial-RNA and matched-image release needed.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "primary availability XML read", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-tourneur-2026-legacyst", "label": "Spatial and single-nuclei transcriptomics reveals idiosyncratic and generic patterns in papillary and anaplastic thyroid cancers", "title": "Spatial and single-nuclei transcriptomics reveals idiosyncratic and generic patterns in papillary and anaplastic thyroid cancers", "citation": { "authors": null, "title": "Spatial and single-nuclei transcriptomics reveals idiosyncratic and generic patterns in papillary and anaplastic thyroid cancers", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13459077/" }, "cancers": [ "THCA" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "spatial-rna" ], "techniques": [ "Spatial Transcriptomics (legacy arrays)" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "platform", "identity", "image-qc", "calibration" ], "accession": "EGAS00001007574 / EGAD00001011365", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC13459077/" ], [ "Data record", "https://zenodo.org/records/8431391" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "original-ready", "depth": "downloaded components checked", "states": [ "public-download", "local-qc" ], "image_finding": "25 PTC original TIFFs indexed and headers checked, about 28k-36k pixels", "molecular_finding": "All 25 PTC Seurat count-column/coordinate label sets exact and finite; legacy ST, not Visium", "next_step": "Overlay and calibration QC for the legacy arrays; section treatment and site unknown; 12 anaplastic sections excluded.", "sections_listed": 25, "study_local_donors": 10 }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "cand-yu2026atlas", "label": "Yu et al. 2026", "title": "A Spatial Atlas of Muscle-Invasive Bladder Cancer Reveals Lineage-Specific Vulnerabilities and Immune Architecture", "citation": { "authors": "Yu K, et al.", "title": "A Spatial Atlas of Muscle-Invasive Bladder Cancer Reveals Lineage-Specific Vulnerabilities and Immune Architecture", "journal": "Cancer Discovery", "year": 2026, "doi": "10.1158/2159-8290.CD-26-0099", "url": "https://doi.org/10.1158/2159-8290.CD-26-0099" }, "cancers": [ "BLCA" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE319536", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://doi.org/10.1158/2159-8290.CD-26-0099" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE319536" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "22 Space Ranger previews", "molecular_finding": "22 exact; one preview has one out-of-frame in-tissue spot flagged", "next_step": "Clinical adjudication against the reported 22-patient denominator; one preview has an out-of-frame spot flagged.", "sections_listed": 22, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-ziblat2024", "label": "Batf3+ DCs and the 4–1BB/4–1BBL axis are required at the effector phase in the tumor microenvironment for PD-1/PD-L1 blockade efficacy", "title": "Batf3+ DCs and the 4–1BB/4–1BBL axis are required at the effector phase in the tumor microenvironment for PD-1/PD-L1 blockade efficacy", "citation": { "authors": null, "title": "Batf3+ DCs and the 4–1BB/4–1BBL axis are required at the effector phase in the tumor microenvironment for PD-1/PD-L1 blockade efficacy", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11229087/" }, "cancers": [ "BLCA" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "spatial-rna" ], "techniques": [ "Visium HD", "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "pathology-review", "image-qc", "calibration" ], "accession": "GSE238145", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11229087/" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE238145" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "original-ready", "depth": "downloaded components checked", "states": [ "public-download", "local-qc" ], "image_finding": "Two 14,054 × 13,447 originals; eight CytAssist TIFFs only 3,000 × 3,000", "molecular_finding": "Two original sections have all expressed spots in positions after explicit unique .1_ to -1_ normalization; extra position rows documented", "next_step": "Original-image overlay and calibration QC; the ten smaller-image regions share eight array areas and need multi-specimen review.", "sections_listed": 12, "study_local_donors": 2 }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "cand-jiang2024meti", "label": "Jiang et al. 2024", "title": "METI: deep profiling of tumor ecosystems by integrating cell morphology and spatial transcriptomics", "citation": { "authors": "Jiang J, et al.", "title": "METI: deep profiling of tumor ecosystems by integrating cell morphology and spatial transcriptomics", "journal": "Nature Communications", "year": 2024, "doi": "10.1038/s41467-024-51708-9", "url": "https://www.nature.com/articles/s41467-024-51708-9" }, "cancers": [ "BLCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "pathology-review" ], "accession": "GSE246011", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41467-024-51708-9" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE246011" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "registration-gap", "depth": "components inspected; join incomplete", "states": [ "author-release", "local-qc" ], "image_finding": "Two bladder TIFFs only 3,000 × 3,000; supplied coordinates extend beyond those pixels", "molecular_finding": "9,029 and 9,963 matrix spots exactly match in-tissue barcodes", "next_step": "Recover original/transform or establish source-backed scaling; TIFF extension is not original-scan proof.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Image scale", "depth": "associated public GEO metadata", "result": "Source-backed scaling is still open; the METI LUAD14C metadata do not supply image coordinates." } ] } }, { "id": "cand-yoshihara2026erbt", "label": "Yoshihara et al. 2026", "title": "Spatial transcriptomics of en bloc transurethral resection of bladder tumor specimens defines an invasive-front gene expression signature", "citation": { "authors": "Yoshihara K, et al.", "title": "Spatial transcriptomics of en bloc transurethral resection of bladder tumor specimens defines an invasive-front gene expression signature", "journal": "npj Precision Oncology", "year": 2026, "doi": "10.1038/s41698-026-01417-x", "url": "https://www.nature.com/articles/s41698-026-01417-x" }, "cancers": [ "BLCA" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "calibration", "he-not-located", "image-qc" ], "accession": "E-GEAD-1186", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41698-026-01417-x" ], [ "Data record", "https://ddbj.nig.ac.jp/public/ddbj_database/gea/experiment/E-GEAD-1000/E-GEAD-1186/" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "technical-gap", "depth": "public download failed", "states": [ "download-failure" ], "image_finding": "DDBJ directory/error response and FTP-host timeout", "molecular_finding": "No package downloaded", "next_step": "Retry authoritative DDBJ/GEA release listing and specimen identifiers; technical failure is not access denial.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "outcome": "preview-ready-partial", "depth": "seven-entry remote ZIP listing and one complete 75.6 MB section package", "findings": "The public DDBJ archive lists seven section packages. Sample1 was read completely: its 2,078 matrix barcodes equal the in-tissue positions, all inside the scaled preview. The CytAssist TIFF is not an original scan.", "next_step": "Check the six other packages, then recover original scans and the clinical scope.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-pribus2026", "label": "Pribus et al. 2026", "title": "Multiomic profiling links L1 retrotransposition to genomic instability and ecDNA in bladder cancer", "citation": { "authors": "Pribus SJ, et al.", "title": "Multiomic profiling links L1 retrotransposition to genomic instability and ecDNA in bladder cancer", "journal": "Nature Communications", "year": 2026, "doi": "10.1038/s41467-026-75399-6", "url": "https://www.nature.com/articles/s41467-026-75399-6" }, "cancers": [ "BLCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located" ], "accession": "GHGAS23497594176126; Zenodo 20085382", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41467-026-75399-6" ], [ "Data record", "https://zenodo.org/records/20085382" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "public listing or archive inventoried", "states": [ "public-download", "local-qc" ], "image_finding": "11.05 GB data ZIP central directory checked; large combined H5AD and derived CNA files", "molecular_finding": "Raw/processed/provenance still need separating; directory includes Gouin/Chen reused data", "next_step": "Inspect metadata and combined measured-count object, original H&E and reuse crosswalk; raw GHGA is a separate permission route.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Package join", "depth": "ZIP central directory; failed selected-member retry", "result": "The 108-entry archive inventory is kept; reading a selected member over the network failed, which is a technical gap." } ] } }, { "id": "cand-xuzhou2023", "label": "Integrated single-cell and spatial transcriptomic profiling reveals higher intratumour heterogeneity and epithelial–fibroblast interactions in recurrent bladder cancer", "title": "Integrated single-cell and spatial transcriptomic profiling reveals higher intratumour heterogeneity and epithelial–fibroblast interactions in recurrent bladder cancer", "citation": { "authors": null, "title": "Integrated single-cell and spatial transcriptomic profiling reveals higher intratumour heterogeneity and epithelial–fibroblast interactions in recurrent bladder cancer", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10366350/" }, "cancers": [ "BLCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "release-unresolved" ], "accession": "OEP004141", "access": { "category": "unresolved", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10366350/" ], [ "Data record", "https://www.biosino.org/node/project/detail/OEP004141" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "technical-gap", "depth": "public download failed", "states": [ "download-failure" ], "image_finding": "Article says processed supporting tables; NODE page 403", "molecular_finding": "No complete spatial package", "next_step": "Inspect supporting tables and recover public NODE listing before inferring author-only access.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public route retry", "depth": "bounded public route retry", "result": "NODE still returns HTTP 403; no processed package was inspected." } ] } }, { "id": "cand-zheng2025", "label": "Unveiling Immune Metabolic Mechanisms in Bladder Cancer: Spatial Profiling Identifies ZFP36 as a Therapeutic Target", "title": "Unveiling Immune Metabolic Mechanisms in Bladder Cancer: Spatial Profiling Identifies ZFP36 as a Therapeutic Target", "citation": { "authors": null, "title": "Unveiling Immune Metabolic Mechanisms in Bladder Cancer: Spatial Profiling Identifies ZFP36 as a Therapeutic Target", "journal": null, "year": null, "doi": null, "url": null }, "cancers": [ "BLCA" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "identity", "he-not-located", "image-qc", "calibration" ], "accession": "GSE285715", "access": { "category": "open", "route": null, "links": [ [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE285715" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "Six previews", "molecular_finding": "All six exact", "next_step": "Donor, site and treatment from the source; original image QC.", "sections_listed": 6, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-lindskrog2023", "label": "Single-nucleus and Spatially Resolved Intratumor Subtype Heterogeneity in Bladder Cancer", "title": "Single-nucleus and Spatially Resolved Intratumor Subtype Heterogeneity in Bladder Cancer", "citation": { "authors": null, "title": "Single-nucleus and Spatially Resolved Intratumor Subtype Heterogeneity in Bladder Cancer", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10175738/" }, "cancers": [ "BLCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled" ], "accession": null, "access": { "category": "controlled", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10175738/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "access-dependent", "depth": "access boundary reached", "states": [ "dac-approval" ], "image_finding": "Primary full text retrieved; controlled route retained", "molecular_finding": "No controlled package accessed", "next_step": "Locate any public processed/original-image alternative; approval needed only for actually controlled files.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-dutreneo", "label": "Grande et al. 2025", "title": "Spatial biomarkers of response to neoadjuvant therapy in muscle-invasive bladder cancer (DUTRENEO)", "citation": { "authors": "Grande E, et al.", "title": "Spatial biomarkers of response to neoadjuvant therapy in muscle-invasive bladder cancer: the DUTRENEO trial", "journal": null, "year": 2025, "doi": "10.1101/2025.02.07.25321742", "url": "https://www.medrxiv.org/content/10.1101/2025.02.07.25321742v1.full" }, "cancers": [ "BLCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "request" ], "accession": "GSE328930 (bulk only); Zenodo 19693316 (Xenium only)", "access": { "category": "open", "route": "Public targeted-RNA data in Zenodo 19693316; the earlier request-only label is corrected", "links": [ [ "Publication", "https://www.medrxiv.org/content/10.1101/2025.02.07.25321742v1.full" ], [ "Data record", "https://pmc.ncbi.nlm.nih.gov/articles/PMC13400163/" ], [ "Targeted RNA data (Zenodo 19693316)", "https://zenodo.org/records/19693316" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "public listing or archive inventoried", "states": [ "public-download", "local-qc" ], "image_finding": "Primary full text corrects old request label: public Zenodo 19693316 now exists", "molecular_finding": "Public 20-sample metadata; 32 GB Xenium ZIP not fully checked", "next_step": "Inspect the targeted expression and centroids and their relation to the H&E; do not infer 20 independent patients.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "outcome": "image-linkage-gap", "depth": "32 GB ZIP central directory plus selected Xenium JSON members", "findings": "The 32 GB archive has 1,457 entries in 20 Xenium sample folders with morphology-focus and per-cycle fluorescence images, which are not H&E; no H&E correspondence is given.", "next_step": "Join the targeted expression and centroids to H&E if a public H&E is released; fluorescence morphology is not a substitute.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-hoefflin2026", "label": "Hoefflin et al. 2026", "title": "Spatial analysis reveals the evolving organization of IDH-mutant glioma", "citation": { "authors": "Hoefflin R, et al.", "title": "Spatial analysis reveals the evolving organization of IDH-mutant glioma", "journal": "Cancer Cell", "year": 2026, "doi": "10.1016/j.ccell.2026.08.005", "url": "https://doi.org/10.1016/j.ccell.2026.08.005" }, "cancers": [ "LGG" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-unverified" ], "accession": "Zenodo 18380571; CODEX Zenodo 21335411; BIA S-BIAD2840", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://doi.org/10.1016/j.ccell.2026.08.005" ], [ "Data record", "https://zenodo.org/records/18380571" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "public listing or archive inventoried", "states": [ "public-download", "local-qc" ], "image_finding": "Public archive has IDH-mutant spatial tar 1.69 GB and reused GBM tar 2.15 GB", "molecular_finding": "Sample/conversion tables inspected; originals not validated", "next_step": "Inspect IDH-mutant image/matrix packages and clinical alias map; reused Ravi GBM is not independent new patients.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "outcome": "bounded-public-work-reuse-known", "depth": "public sample list, explicit 25-row Ravi conversion table and archive prefixes", "findings": "The public sample list declares 25 relabelled glioblastoma samples reused from Ravi et al.; the IDH-mutant and glioblastoma archives were not fully read.", "next_step": "Inspect a selected IDH-mutant package and the source donor map; the reused Ravi samples are not new patients.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-greenwald2024", "label": "Greenwald et al. 2024", "title": "Integrative spatial analysis reveals a multi-layered organization of glioblastoma", "citation": { "authors": "Greenwald AC, et al.", "title": "Integrative spatial analysis reveals a multi-layered organization of glioblastoma", "journal": "Cell", "year": 2024, "doi": "10.1016/j.cell.2024.03.029", "url": "https://doi.org/10.1016/j.cell.2024.03.029" }, "cancers": [ "LGG", "GBM" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "identity", "treatment-review", "pathology-review", "he-not-located", "calibration", "image-qc" ], "accession": "GSE237183; Zenodo 12624860", "access": { "category": "open", "route": "public processed GEO", "links": [ [ "Publication", "https://doi.org/10.1016/j.cell.2024.03.029" ], [ "Data record", "https://zenodo.org/records/12624860" ], [ "GEO series", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237183" ], [ "Author repository (Visium image archive link)", "https://github.com/tiroshlab/Spatial_Glioma" ], [ "Clinical Table S1", "https://www.cell.com/cms/10.1016/j.cell.2024.03.029/attachment/89b1c464-df78-4b1d-b0c4-22ff214799c7/mmc1.pdf" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Visium study of glioma organisation with 19 sections: 13 IDH-wildtype glioblastoma sections from five donor labels and six IDH-mutant sections (astrocytoma and oligodendroglioma) from six donor labels. Repeated regions of one donor (ZH881) are one donor label, not separate patients. All 15 original images in the author-linked Visium image archive were retrieved; 14 have geometrically supported counterparts among the GEO sections, and five GEO sections have no original in that archive. The two ZH881 bulk originals match the opposite GEO labels (ZH881_1A_bulk.tif matches GSM7596598 and ZH881_1B_bulk.tif matches GSM7596597); this is an inferred correspondence awaiting author confirmation, and the source labels are kept. In the public clinical Table S1, ZH1041_T1 is CODEX-only, the ZH1019 rows carry the patient ID ZH1007 although age, MGMT status and location differ, BWH23 is reported as IDH-mutant oligodendroglioma grade 4 and BWH28 as astrocytoma grade 2/3; treatment and recurrence are not reported. The Zenodo 12624860 H&E archive accompanies the CODEX data and is a separate serial-section resource, not the Visium image route.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 13, "IDH-wildtype glioblastoma sections", "GEO series", "GBM" ], [ 5, "IDH-wildtype donor labels", "GEO series", "GBM" ], [ 6, "IDH-mutant glioma sections", "GEO series", "LGG" ], [ 6, "IDH-mutant donor labels", "GEO series", "LGG" ], [ 19, "sections in the study", "GEO series" ], [ 14, "GEO sections with a matched original image", "image correspondence check" ], [ 5, "GEO sections without an original image in the author archive", "image correspondence check" ] ], "notes": [ "ZH881 repeated regions are one donor label, not separate patients", "Preserve IDH-mutant astrocytoma and oligodendroglioma labels", "Review recurrence/treatment and donor crosswalk; do not call 13 sections 13 patients", "ZH881 bulk labels are crossed by inference: keep the source filenames and GEO labels until the authors confirm", "The ZH1019 rows carry the conflicting patient ID ZH1007; keep five provisional IDH-wildtype donor labels", "BWH23 (reported oligodendroglioma grade 4) and BWH28 (astrocytoma grade 2/3) need diagnosis and grade review", "Treatment and recurrence are not reported", "Keep CODEX-associated H&E separate from the Visium images", "Twelve sections have directly matched original images; the two with inferred crossed labels and the five without originals are shown at preview level" ], "spatial_review": { "id": "glioma-greenwald-gse237183", "date": "2026-10-15", "analysis_cohort": "GLIOMA", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium", "role": "candidate resource", "image_status": "All 15 originals in the author-linked Visium archive retrieved (about 3,800 × 4,200 to 17,000 × 17,000 pixels); 14 match GEO sections geometrically, with the ZH881 bulk labels crossed by inference; five GEO sections have no original. TIFF DPI tags are not scanner calibration.", "treatment_status": "not reported in clinical Table S1; recurrence unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "route_review": { "date": "2026-10-15", "status": "14 of 19 sections matched to original images; labels and clinical issues flagged", "states": [ "public-download", "author-release", "local-qc" ], "next_step": "Ask the study team for the five missing originals, confirmation of the crossed ZH881 labels, the ZH1019 patient ID, BWH23 and BWH28 diagnosis and grade, scanner calibration and treatment and recurrence; then image and pathology QC.", "sections_with_matching_coordinates": 19 } }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "cand-webb2025", "label": "Webb et al. 2025", "title": "Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas", "citation": { "authors": "Webb MG, et al.", "title": "Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas", "journal": "Nature Communications", "year": 2025, "doi": "10.1038/s41467-025-59805-z", "url": "https://doi.org/10.1038/s41467-025-59805-z" }, "cancers": [ "LGG" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE242352; EGA EGAD50000001394", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://doi.org/10.1038/s41467-025-59805-z" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE242352" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "17 previews; two sections have out-of-frame coordinates flagged", "molecular_finding": "All 17 exact", "next_step": "Donor independence and two image-frame checks; recurrent, oligodendroglioma and astrocytoma labels are kept.", "sections_listed": 17, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-snu2026", "label": "Sonpatki et al. 2026", "title": "A spatially resolved human glioblastoma atlas reveals distinct cellular and molecular patterns of anatomical niches", "citation": { "authors": "Sonpatki P, et al.", "title": "A spatially resolved human glioblastoma atlas reveals distinct cellular and molecular patterns of anatomical niches", "journal": "Nature Communications", "year": 2026, "doi": "10.1038/s41467-026-69716-2", "url": "https://doi.org/10.1038/s41467-026-69716-2" }, "cancers": [ "LGG", "GBM" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE", "Visium", "Xenium" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "package-unverified", "identity", "treatment-review", "he-not-located" ], "accession": "Zenodo 17572905; PRJNA1337938; Zenodo 17622242", "access": { "category": "open", "route": "public Zenodo records and UCSC Cell Browser", "links": [ [ "Publication", "https://doi.org/10.1038/s41467-026-69716-2" ], [ "Data record", "https://zenodo.org/records/17572905" ], [ "Xenium release", "https://zenodo.org/records/17622242" ], [ "Cell browser", "https://cells.ucsc.edu/?ds=multiomic-gbm" ], [ "Author repository", "https://github.com/nameetas/TSKGA" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Glioma anatomical-niche atlas with 32 Visium sections from 17 patients: 13 with glioblastoma (28 sections), three with IDH-mutant astrocytoma (two grade 3 and one grade 4; three sections) and one normal-brain control from a central-neurocytoma patient. Twenty-seven sections are FFPE and five fresh frozen. Four glioblastoma patients (SNU18, SNU21, SNU25 and SNU33) also have Xenium data and are not additional patients. Section SNU25B is assigned to SNU25 provisionally, following the publication and spot metadata, although the author slide table lists SNU26. The eight public Visium archive packages contain Space Ranger outputs and previews without a separately listed original scan, so they do not establish image coverage of all 32 sections. All five Xenium archives are inventoried, including SNU21's nested analysis archive; their morphology TIFFs are fluorescence images, not H&E. The data statement labels Zenodo 16505469 as Ravi 2022, but that record belongs to the Ravikumar/Al-Holou study (see related leads); which reused dataset the atlas analysed is unresolved. Released in Zenodo 17572905 (Visium) and 17622242 (Xenium), with a UCSC Cell Browser view.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 17, "patients in all, including one normal-brain control", "publication and spot metadata" ], [ 13, "patients with glioblastoma", "publication and spot metadata", "GBM" ], [ 28, "glioblastoma sections", "publication and spot metadata", "GBM" ], [ 3, "patients with IDH-mutant astrocytoma", "publication and spot metadata", "LGG" ], [ 3, "IDH-mutant astrocytoma sections", "publication and spot metadata", "LGG" ], [ 1, "normal-brain control patient (central neurocytoma), one section", "publication and spot metadata" ], [ 32, "Visium sections in all", "publication" ], [ 27, "FFPE Visium sections", "publication" ], [ 5, "fresh-frozen Visium sections", "publication" ], [ 4, "Xenium patients, all also profiled with Visium", "publication" ] ], "notes": [ "Deduplicate Visium/Xenium and other reused datasets", "Xenium patients overlap the Visium patients; do not add them", "SNU25B is provisionally SNU25; the author slide table says SNU26", "The eight Visium archives hold outputs and previews only; they are not image coverage of all 32 sections", "Xenium morphology TIFFs are fluorescence images, not H&E", "Zenodo 16505469 is the Ravikumar/Al-Holou release, not Ravi 2022; the atlas's actual reused input is unresolved", "Match original images, matrices and transforms to every section", "Treatment and recurrence are not reported" ], "spatial_review": { "id": "glioma-2026-niche-atlas", "date": "2026-10-15", "analysis_cohort": "GLIOMA", "assay_classes": [ "whole-transcriptome", "targeted-rna" ], "platform": "Visium plus Xenium", "role": "candidate resource", "image_status": "Eight public Visium archive packages inventoried: Space Ranger outputs and previews, no separately listed original scan; five Xenium archives inventoried, with fluorescence morphology TIFFs only; complete section–patient–image linkage unresolved", "treatment_status": "not reported in the clinical table; primary or recurrent status needs a per-patient crosswalk", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "route_review": { "date": "2026-10-15", "status": "Patient and diagnosis denominator resolved; image coverage and linkage unresolved", "states": [ "public-download", "author-release", "local-qc" ], "next_step": "Ask the study team for the per-section count, image and patient crosswalk, original H&E beyond previews and fluorescence images, treatment and recurrence, and which reused dataset was analysed.", "sections_with_matching_coordinates": 1 } } }, { "id": "cand-ritternepsta2025", "label": "Ritter et al. 2025", "title": "Spatially resolved transcriptomics and graph-based deep learning improve accuracy of routine CNS tumor diagnostics", "citation": { "authors": "Ritter M, et al.", "title": "Spatially resolved transcriptomics and graph-based deep learning improve accuracy of routine CNS tumor diagnostics", "journal": "Nature Cancer", "year": 2025, "doi": "10.1038/s43018-024-00904-z", "url": "https://doi.org/10.1038/s43018-024-00904-z" }, "cancers": [ "LGG", "GBM" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "Zenodo 14064047", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://doi.org/10.1038/s43018-024-00904-z" ], [ "Data record", "https://zenodo.org/records/14064047" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "All 55 ZIPs checked; previews max 2,000 px", "molecular_finding": "All 55 exact; clinical table links diagnoses, includes duplicate 110640 row", "next_step": "Donor independence; 15 gliosarcoma sections are kept as glioblastoma variants, unrelated to TCGA-SARC; other CNS tumour types excluded.", "sections_listed": 46, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-tang2025", "label": "Tang et al. 2025", "title": "Protein-based classification reveals an immune-hot subtype in IDH mutant astrocytoma with worse prognosis", "citation": { "authors": "Tang J, et al.", "title": "Protein-based classification reveals an immune-hot subtype in IDH mutant astrocytoma with worse prognosis", "journal": "Cancer Cell", "year": 2025, "doi": "10.1016/j.ccell.2025.08.006", "url": "https://doi.org/10.1016/j.ccell.2025.08.006" }, "cancers": [ "LGG" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium HD" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-unverified", "pathology-review" ], "accession": "GSA HRA012868/HRA012869/HRA012870/HRA012903; author STP portal", "access": { "category": "unresolved", "route": null, "links": [ [ "Publication", "https://doi.org/10.1016/j.ccell.2025.08.006" ], [ "Data record", "https://wang-lab.hkust.edu.hk/software/STP" ], [ "Public data portal", "http://lfz178.ust.hk:8088/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "technical-gap", "depth": "public download failed", "states": [ "download-failure" ], "image_finding": "Public STP page not a usable assay listing", "molecular_finding": "Unverified", "next_step": "Resolve study-specific processed-data/source image links; software page is not package evidence.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "outcome": "public-portal-link-resolved", "depth": "source portal redirect and destination page read", "findings": "The software link now redirects to a public portal; no package-to-section join was inspected.", "next_step": "Inspect the portal's dataset and file metadata; raw GSA routes and processed spatial data stay separate.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-longitudinal2026", "label": "Spatially resolved gene expression and tumour-microenvironment interactions across malignant transformation in IDH-mutant glioma", "title": "Spatially resolved gene expression and tumour-microenvironment interactions across malignant transformation in IDH-mutant glioma", "citation": { "authors": null, "title": "Spatially resolved gene expression and tumour-microenvironment interactions across malignant transformation in IDH-mutant glioma", "journal": null, "year": null, "doi": null, "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE318238" }, "cancers": [ "LGG" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "pathology-review", "image-qc", "calibration" ], "accession": "GSE318238; GSM9490659", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE318238" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "Three molecularly checked preview packages plus a separate unjoined multi-image sample", "molecular_finding": "Three exact", "next_step": "Same-patient timeline and the crosswalk of a fourth sample.", "sections_listed": 3, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-he2024", "label": "He et al. 2024", "title": "Single-cell and spatial transcriptome assays reveal heterogeneity in gliomas through stress responses and pathway alterations", "citation": { "authors": "He Z, et al.", "title": "Single-cell and spatial transcriptome assays reveal heterogeneity in gliomas through stress responses and pathway alterations", "journal": "Frontiers in Immunology", "year": 2024, "doi": "10.3389/fimmu.2024.1452172", "url": "https://doi.org/10.3389/fimmu.2024.1452172" }, "cancers": [ "LGG" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "pathology-review", "he-not-located", "image-qc", "calibration" ], "accession": "GSE270355", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://doi.org/10.3389/fimmu.2024.1452172" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE270355" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "Four archive previews; separately listed RAW PNGs are only 867-918 by 91-104 pixels, not original scans", "molecular_finding": "Four exact", "next_step": "Original scans and the donor, histology, grade and reuse crosswalk.", "sections_listed": 4, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-kuchroosparc2022", "label": "Kuchroo et al. 2022", "title": "Glioma spatial atlas (spARC)", "citation": { "authors": "Kuchroo M, et al.", "title": "spARC recovers human glioma spatial signaling networks with graph filtering", "journal": null, "year": 2022, "doi": "10.1101/2022.08.24.505139", "url": "https://doi.org/10.1101/2022.08.24.505139" }, "cancers": [ "LGG" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "release-unresolved" ], "accession": null, "access": { "category": "unresolved", "route": null, "links": [ [ "Publication", "https://doi.org/10.1101/2022.08.24.505139" ], [ "Data record", "https://github.com/KrishnaswamyLab/spARC" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "code-only-lead", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Public GitHub tree inspected", "molecular_finding": "No source-backed original-image/count package verified", "next_step": "Identify released measured specimens behind method demonstration and deduplicate reused studies.", "sections_listed": null, "study_local_donors": null } }, { "id": "cand-gaspardboulin2025", "label": "Gaspard-Boulinc et al. 2025", "title": "EPCO-18. Unravelling IDH-mutant gliomas heterogeneities with spatial transcriptomics", "citation": { "authors": "Gaspard-Boulinc L, et al.", "title": "EPCO-18. Unravelling IDH-mutant gliomas heterogeneities with spatial transcriptomics", "journal": "Neuro-Oncology", "year": 2025, "doi": "10.1093/neuonc/noaf201.0018", "url": "https://doi.org/10.1093/neuonc/noaf201.0018" }, "cancers": [ "LGG" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "release-unresolved" ], "accession": "No public accession identified", "access": { "category": "unresolved", "route": null, "links": [ [ "Publication", "https://doi.org/10.1093/neuonc/noaf201.0018" ], [ "Data record", "https://academic.oup.com/neuro-oncology/article/27/Supplement_5/v5/8318223" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "release-unresolved", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Conference abstract/publisher access does not supply package", "molecular_finding": "Unverified", "next_step": "Find final publication and actionable accession before counts.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Release search", "depth": "bounded Europe PMC title search", "result": "A bounded literature search found no measured spatial package with original images; other routes may still need review." }, { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-spatch-hcc", "label": "Ren et al. 2025", "title": "Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors (liver sample)", "citation": { "authors": "Ren P, et al.", "title": "Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors", "journal": "Nature Communications", "year": 2025, "doi": "10.1038/s41467-025-64292-3", "url": "https://www.nature.com/articles/s41467-025-64292-3" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium HD" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "calibration" ], "accession": "S-BIAD1900; HRA011129", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41467-025-64292-3" ], [ "Images (BioImage Archive S-BIAD1900)", "https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1900" ], [ "Code (Zenodo 16992659)", "https://zenodo.org/records/16992659" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "public listing or archive inventoried", "states": [ "public-download", "local-qc" ], "image_finding": "Five-platform HCC originals listed in S-BIAD1900", "molecular_finding": "RNA/coordinate matching unverified; CODEX separate", "next_step": "Join HCC assays to measured expression/coordinates; preserve multi-assay overlap and serial/same-section relation.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Package join", "depth": "public file-list metadata", "result": "The same 36-file list does not establish the HCC RNA and coordinate join." } ] } }, { "id": "cand-gse238264", "label": "Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence", "title": "Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence", "citation": { "authors": null, "title": "Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10506285/" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "treated", "he-not-located", "image-qc", "calibration" ], "accession": "GSE238264", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10506285/" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE238264" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "Seven archive previews", "molecular_finding": "All seven exact", "next_step": "Original scans; all seven donors were treated with cabozantinib and nivolumab.", "sections_listed": 7, "study_local_donors": 7 }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-gse281759", "label": "Multiomics and multi-region spatial transcriptome analysis reveal cellular networks and pathways associated with hepatocellular carcinoma recurrence", "title": "Multiomics and multi-region spatial transcriptome analysis reveal cellular networks and pathways associated with hepatocellular carcinoma recurrence", "citation": { "authors": null, "title": "Multiomics and multi-region spatial transcriptome analysis reveal cellular networks and pathways associated with hepatocellular carcinoma recurrence", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13087693/" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE281759", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC13087693/" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE281759" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "17 previews, one adjacent-normal record", "molecular_finding": "All 17 exact", "next_step": "Donor total (the B0013 and B013 aliases conflict); regions, recurrent versus primary labels and one normal section are kept.", "sections_listed": 17, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-times-hra006579", "label": "Jia et al. 2025", "title": "Spatial immune scoring system predicts hepatocellular carcinoma recurrence", "citation": { "authors": "Jia G, et al.", "title": "Spatial immune scoring system predicts hepatocellular carcinoma recurrence", "journal": "Nature", "year": 2025, "doi": "10.1038/s41586-025-08668-x", "url": "https://www.nature.com/articles/s41586-025-08668-x" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "package-unverified" ], "accession": "HRA006579; OSF db3uf", "access": { "category": "unresolved", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41586-025-08668-x" ], [ "Data record", "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA006579" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "release-unresolved", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Primary publication/HRA route inspected at available metadata level", "molecular_finding": "No matched processed image package verified", "next_step": "Resolve processed release and original-image coordinates separately from HRA raw access.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Release search", "depth": "bounded Europe PMC title search", "result": "A bounded literature search found no measured spatial package with original images; other routes may still need review." }, { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-wu2025-zenodo", "label": "Spatial multi-omics and deep learning reveal fingerprints of immunotherapy response and resistance in hepatocellular carcinoma", "title": "Spatial multi-omics and deep learning reveal fingerprints of immunotherapy response and resistance in hepatocellular carcinoma", "citation": { "authors": null, "title": "Spatial multi-omics and deep learning reveal fingerprints of immunotherapy response and resistance in hepatocellular carcinoma", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12259099/" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "serial-section", "treated", "he-not-located", "image-qc", "calibration" ], "accession": "Zenodo 19123188 (earlier version 15392699)", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12259099/" ], [ "Data record", "https://zenodo.org/records/19123188" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "linkage-gap", "depth": "components inspected; join incomplete", "states": [ "local-qc" ], "image_finding": "36 large H&E JPEGs are CODEX-region named; nested 22 Visium previews also present", "molecular_finding": "104,418-spot measured H5AD with 22 sample labels/11 patient IDs and 28 extra coordinate CSVs inspected", "next_step": "Join RNA sections to 22 preview image libraries and independent position tables; do not substitute 36 CODEX-region H&E images for 22 Visium sections.", "sections_listed": null, "study_local_donors": 11 }, "followup_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "complete source H5AD row/image-library/scale checks; independent 28 CSV join unresolved", "findings": "The source H5AD holds 104,418 expression rows and 22 named image libraries; rows, observation index and spatial coordinates align, and every coordinate falls inside its supplied preview. The 36 CODEX-region H&E images are not Visium originals.", "next_step": "Recover the original H&E of the assayed sections, join the 28 separate position tables independently and establish a public alias for the 11 source patients.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-wu2021-hcc", "label": "Wu et al. 2021", "title": "A comprehensive analysis of the spatial architecture of primary liver cancer", "citation": { "authors": "Wu R, et al.", "title": "Comprehensive analysis of spatial architecture in primary liver cancer", "journal": "Science Advances", "year": 2021, "doi": "10.1126/sciadv.abg3750", "url": "https://doi.org/10.1126/sciadv.abg3750" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located" ], "accession": "HRA000437; author Lifeome portal", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://doi.org/10.1126/sciadv.abg3750" ], [ "Data record", "http://lifeome.net/supp/livercancer-st/data.htm" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "technical-gap", "depth": "public download failed", "states": [ "download-failure" ], "image_finding": "Author lists HCC/ICC/cHC archives; selected HCC archive truncates during first member", "molecular_finding": "No complete selected matrix/image package", "next_step": "Recover intact HCC-only release; keep mixed/cholangiocarcinoma out and preserve sample/donor repeats.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public route retry", "depth": "bounded public route retry", "result": "The Lifeome server refuses connections; no archive was inspected." } ] } }, { "id": "cand-he2024-new4plc", "label": "Jing et al. 2024", "title": "Spatial multiomics reveals a subpopulation of fibroblasts associated with cancer stemness in human hepatocellular carcinoma", "citation": { "authors": "Jing Sy, et al.", "title": "Spatial multiomics reveals a subpopulation of fibroblasts associated with cancer stemness in human hepatocellular carcinoma", "journal": "Genome Medicine", "year": 2024, "doi": "10.1186/s13073-024-01367-8", "url": "https://link.springer.com/article/10.1186/s13073-024-01367-8" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled" ], "accession": "OMIX006870", "access": { "category": "controlled", "route": null, "links": [ [ "Publication", "https://link.springer.com/article/10.1186/s13073-024-01367-8" ], [ "Data record", "https://ngdc.cncb.ac.cn/omix/release/OMIX006870" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "access-dependent", "depth": "access boundary reached", "states": [ "dac-approval" ], "image_finding": "OMIX/publication metadata route", "molecular_finding": "No controlled file accessed", "next_step": "Public processed/original-image route or formal access decision; preserve four primary-liver histologies.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-fan2024-hra006757", "label": "Fan et al. 2024", "title": "Spatial transcriptomics of hepatocellular carcinoma", "citation": { "authors": "Fan G, et al.", "title": "Single-cell and spatial analyses revealed the co-location of cancer stem cells and SPP1+ macrophage in hypoxic region that determines the poor prognosis in hepatocellular carcinoma", "journal": "npj Precision Oncology", "year": 2024, "doi": "10.1038/s41698-024-00564-3", "url": "https://www.nature.com/articles/s41698-024-00564-3" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled" ], "accession": "HRA006757", "access": { "category": "controlled", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41698-024-00564-3" ], [ "Data record", "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA006757" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "access-dependent", "depth": "access boundary reached", "states": [ "dac-approval" ], "image_finding": "HRA/publication metadata route", "molecular_finding": "No controlled file accessed", "next_step": "Resolve processed matrix/image/coordinates separately from raw permission.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-jgad000422-hcc", "label": "Murai et al. 2022", "title": "Multiomics identifies the link between intratumor steatosis and the exhausted tumor immune microenvironment in hepatocellular carcinoma", "citation": { "authors": "Murai H, et al.", "title": "Multiomics identifies the link between intratumor steatosis and the exhausted tumor immune microenvironment in hepatocellular carcinoma", "journal": "Hepatology", "year": 2022, "doi": "10.1002/hep.32573", "url": "https://doi.org/10.1002/hep.32573" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled" ], "accession": "JGAD000422; JGAS000311; hum0286v2", "access": { "category": "controlled", "route": null, "links": [ [ "Publication", "https://doi.org/10.1002/hep.32573" ], [ "Data record", "https://humandbs-production.ddbj.nig.ac.jp/en/dataset/JGAD000422" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "access-dependent", "depth": "access boundary reached", "states": [ "dac-approval" ], "image_finding": "Authoritative Japanese controlled dataset route", "molecular_finding": "No controlled file accessed", "next_step": "Obtain approved access or public processed alternative.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-egad50000002122", "label": "10x Visium Spatial Transcriptomics of 61 Human HCC Samples", "title": "10x Visium Spatial Transcriptomics of 61 Human HCC Samples", "citation": { "authors": null, "title": "10x Visium Spatial Transcriptomics of 61 Human HCC Samples", "journal": null, "year": null, "doi": null, "url": null }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled" ], "accession": "EGAD50000002122", "access": { "category": "controlled", "route": null, "links": [ [ "Data record", "https://ega-archive.org/datasets/EGAD50000002122" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "access-dependent", "depth": "access boundary reached", "states": [ "dac-approval" ], "image_finding": "Authoritative EGA metadata route", "molecular_finding": "No controlled file accessed", "next_step": "Approved access or public processed alternative, with specimen/image crosswalk.", "sections_listed": null, "study_local_donors": null } }, { "id": "cand-egad50000001506", "label": "Targeting Treg–fibroblast interaction to enhance immunotherapy in SLD-related HCC", "title": "Targeting Treg–fibroblast interaction to enhance immunotherapy in SLD-related HCC", "citation": { "authors": null, "title": "Targeting Treg–fibroblast interaction to enhance immunotherapy in SLD-related HCC", "journal": null, "year": null, "doi": null, "url": "https://gut.bmj.com/content/early/2025/07/30/gutjnl-2025-335084" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled" ], "accession": "EGAD50000001506; EGAS50000001034", "access": { "category": "controlled", "route": null, "links": [ [ "Publication", "https://gut.bmj.com/content/early/2025/07/30/gutjnl-2025-335084" ], [ "Data record", "https://ega-archive.org/datasets/EGAD50000001506" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "access-dependent", "depth": "access boundary reached", "states": [ "dac-approval" ], "image_finding": "EGA/publication metadata route", "molecular_finding": "No controlled file accessed", "next_step": "Approved access or public processed alternative; original-image promise must be checked separately.", "sections_listed": null, "study_local_donors": null } }, { "id": "cand-adapa2025-hd", "label": "Spatial Transcriptomics Reveals Distinct Architectures but Shared Vulnerabilities in Primary and Metastatic Liver Tumors", "title": "Spatial Transcriptomics Reveals Distinct Architectures but Shared Vulnerabilities in Primary and Metastatic Liver Tumors", "citation": { "authors": null, "title": "Spatial Transcriptomics Reveals Distinct Architectures but Shared Vulnerabilities in Primary and Metastatic Liver Tumors", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12523610/" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium HD" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "release-unresolved" ], "accession": "Humanaccessionnotidentified", "access": { "category": "unresolved", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12523610/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "release-unresolved", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Primary full text describes two-specimen HD pilot, primary HCC versus liver metastasis", "molecular_finding": "No actionable measured package verified", "next_step": "Resolve original data accession and metastatic histology; do not pool liver metastasis as HCC.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Release search", "depth": "bounded Europe PMC title search", "result": "A bounded literature search found no measured spatial package with original images; other routes may still need review." }, { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-gse283406", "label": "Deep versus standard spatial transcriptomic sequencing", "title": "Deep versus standard spatial transcriptomic sequencing", "citation": { "authors": null, "title": "Deep versus standard spatial transcriptomic sequencing", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11974817/" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located" ], "accession": "GSE283406; GSE283404/405", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11974817/" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE283406" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "coordinate-gap", "depth": "components inspected; join incomplete", "states": [ "author-release", "local-qc" ], "image_finding": "Four preview images/count matrices; two tissues sequenced on two platforms", "molecular_finding": "GEO lists no position/scale file in four packages", "next_step": "Recover two physical-section coordinate/scale crosswalk; do not count platform resequencing as four independent sections/patients.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Coordinate join", "depth": "complete GEO sample metadata; primary XML", "result": "GEO sample metadata and positions do not resolve the physical-section, grid and scale association." } ] } }, { "id": "cand-prjna858545-hcc", "label": "Lau et al. 2022", "title": "Spatial Transcriptomic of HCC and CRC Patients with COVID-19 Co-Morbidity", "citation": { "authors": "Lau MC, et al.", "title": "Case report: Understanding the impact of persistent tissue-localization of SARS-CoV-2 on immune response activity via spatial transcriptomic analysis of two cancer patients with COVID-19 co-morbidity", "journal": "Frontiers in Immunology", "year": 2022, "doi": "10.3389/fimmu.2022.978760", "url": "https://doi.org/10.3389/fimmu.2022.978760" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "package-unverified", "identity" ], "accession": "PRJNA858545; Figshare 21061990", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://doi.org/10.3389/fimmu.2022.978760" ], [ "Data record", "https://figshare.com/articles/figure/H_E_images_for_the_Spatial_Transcriptomics_10X_Visium_samples_deposited_in_the_BioProject_PRJNA858545/21061990" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "public listing or archive inventoried", "states": [ "public-download", "local-qc" ], "image_finding": "Two original-image candidates in public Figshare; file/API metadata retrieved", "molecular_finding": "Processed RNA/coordinate linkage not verified", "next_step": "Join images to actual BioProject spatial samples and processed counts/positions; raw SRA alone insufficient.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Package join", "depth": "complete public Figshare API metadata", "result": "Figshare lists four public images (HCC, HCC-adjacent, CRC and CRC-adjacent); their RNA, coordinate and sample association is unresolved." } ] } }, { "id": "cand-xin2022-hcc", "label": "Spatial maps of hepatocellular carcinoma transcriptomes reveal spatial expression patterns in tumor immune microenvironment", "title": "Spatial maps of hepatocellular carcinoma transcriptomes reveal spatial expression patterns in tumor immune microenvironment", "citation": { "authors": null, "title": "Spatial maps of hepatocellular carcinoma transcriptomes reveal spatial expression patterns in tumor immune microenvironment", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9169356/" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "release-unresolved" ], "accession": null, "access": { "category": "unresolved", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC9169356/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "release-unresolved", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Primary full text confirms two fresh HCC tissues", "molecular_finding": "No released complete package established", "next_step": "Find an actionable processed/image accession or later author release.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Release search", "depth": "bounded Europe PMC title search", "result": "A bounded literature search found no measured spatial package with original images; other routes may still need review." }, { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-li2025-caf", "label": "Spatial Transcriptomics and snRNA-seq Expose CAF Niches Orchestrating Dual Stromal-Immune Barriers in Hepatocellular Carcinoma", "title": "Spatial Transcriptomics and snRNA-seq Expose CAF Niches Orchestrating Dual Stromal-Immune Barriers in Hepatocellular Carcinoma", "citation": { "authors": null, "title": "Spatial Transcriptomics and snRNA-seq Expose CAF Niches Orchestrating Dual Stromal-Immune Barriers in Hepatocellular Carcinoma", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12752642/" }, "cancers": [ "LIHC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "request" ], "accession": null, "access": { "category": "request", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12752642/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "author-release", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Primary article explicitly says on reasonable request", "molecular_finding": "No public matched package", "next_step": "Processed RNA, coordinates, images and clinical/region map require release.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "primary availability XML read", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-takano-suzuki-2024", "label": "Takano et al. 2024", "title": "Spatially resolved gene expression profiling of tumor microenvironment reveals key steps of lung adenocarcinoma development", "citation": { "authors": "Takano Y, et al.", "title": "Spatially resolved gene expression profiling of tumor microenvironment reveals key steps of lung adenocarcinoma development", "journal": "Nature Communications", "year": 2024, "doi": "10.1038/s41467-024-54671-7", "url": "https://www.nature.com/articles/s41467-024-54671-7" }, "cancers": [ "LUAD" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "calibration", "image-qc" ], "accession": "JGAS000613 / JGAD000742 / hum0394-v1", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41467-024-54671-7" ], [ "Data record", "https://kero.hgc.jp/Ad-SpatialAnalysis_2024.html" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "original-ready", "depth": "downloaded components checked", "states": [ "public-download", "local-qc" ], "image_finding": "One original 10,418 × 11,237 TIFF in selected LUAD3B component set", "molecular_finding": "2,876 expression barcodes exactly match in-tissue positions and lie inside original frame", "next_step": "Only LUAD3B is checked; the rest of the study and image calibration remain (the 72 DPI tag is not a micron scale).", "sections_listed": 1, "study_local_donors": 1 }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "cand-dezuani-cvejic-2024", "label": "De Zuani et al. 2024", "title": "Single-cell and spatial transcriptomics analysis of non-small cell lung cancer", "citation": { "authors": "De Zuani M, et al.", "title": "Single-cell and spatial transcriptomics analysis of non-small cell lung cancer", "journal": "Nature Communications", "year": 2024, "doi": "10.1038/s41467-024-48700-8", "url": "https://www.nature.com/articles/s41467-024-48700-8" }, "cancers": [ "LUAD", "LUSC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "identity", "treatment-review", "image-qc", "calibration" ], "accession": "E-MTAB-13530", "access": { "category": "open", "route": "public processed matrices/spatial archives; ENA raw reads", "links": [ [ "Publication", "https://www.nature.com/articles/s41467-024-48700-8" ], [ "Data record", "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-13530" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Visium fresh-frozen atlas of non-small cell lung cancer with 40 sections in all, 20 of them tumour sections, across adenocarcinoma, squamous, unspecified NSCLC and healthy donors. The LUSC subset is Patients 11 and 19: six tumour sections and four adjacent-normal sections. The publication's Supplementary Data 1 gives Patient 11 as T2b N0 M0 and Patient 19 as T3 N0 M0; prior treatment is not reported. All ten LUSC sections have expression barcodes that match their tissue coordinates exactly, but their image archives contain only outputs of about 2,000 pixels; original scans were not found.", "compartments": [ "tumour-unspecified", "solid-normal", "normal" ], "reported": [ [ 2, "LUSC donors (Patients 11 and 19)", "SDRF, deduplicated", "LUSC" ], [ 6, "LUSC tumour sections", "SDRF, deduplicated", "LUSC" ], [ 4, "LUSC adjacent-normal sections", "SDRF, deduplicated", "LUSC" ], [ 40, "sections in the complete study, all histologies", "SDRF, deduplicated" ], [ 20, "tumour sections in the complete study", "SDRF, deduplicated" ] ], "notes": [ "Use Patient 11 and Patient 19 only for LUSC", "Preserve four adjacent sections outside tumour counts", "SDRF staging fields contain inconsistent values; do not interpret each row as valid TNM", "Staging from Supplementary Data 1: Patient 11 T2b N0 M0, Patient 19 T3 N0 M0", "Prior treatment is not reported", "Matched data with preview image: 10 checked section packages, not yet listed as individual section records" ], "spatial_review": { "id": "lusc-emtab13530", "date": "2026-10-15", "analysis_cohort": "LUSC", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium fresh frozen", "role": "candidate resource", "image_status": "All ten LUSC section packages checked: exact barcode-coordinate agreement; image archives contain 2,000-pixel outputs only; original scans not found", "treatment_status": "not reported; staging resolved from Supplementary Data 1", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": { "tumour_sample_ids": [ "P11_T1", "P11_T2", "P11_T3", "P11_T4", "P19_T1", "P19_T2" ], "adjacent_sample_ids": [ "P11_B1", "P11_B2", "P19_B1", "P19_B2" ] }, "route_review": { "date": "2026-10-15", "status": "Ten LUSC section packages checked; preview images only", "states": [ "public-download", "author-release", "local-qc" ], "next_step": "Ask the study team for original scans and the prior treatment of Patients 11 and 19.", "sections_with_matching_coordinates": 10 } }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-zhao-htapp-2025", "label": "Zhao et al. 2025", "title": "A cellular and spatial atlas of TP53-associated tissue remodeling defines a multicellular tumor ecosystem in lung adenocarcinoma", "citation": { "authors": "Zhao W, et al.", "title": "A cellular and spatial atlas of TP53-associated tissue remodeling defines a multicellular tumor ecosystem in lung adenocarcinoma", "journal": "Nature Cancer", "year": 2025, "doi": "10.1038/s43018-025-01053-7", "url": "https://www.nature.com/articles/s43018-025-01053-7" }, "cancers": [ "LUAD" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "calibration", "identity" ], "accession": "HTAN HTAPP; Zenodo 16546233 (version 19559522)", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s43018-025-01053-7" ], [ "Data record", "https://zenodo.org/records/19559522" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "public listing or archive inventoried", "states": [ "public-download", "local-qc" ], "image_finding": "20 original TIFF members indexed remotely in 30.7 GB ZIP; 8 donor-prefix labels", "molecular_finding": "18.9 GB processed ZIP contains spatial_list.Rda (2.70 GB) and image/source folders", "next_step": "Extract spatial_list and join the exact 20 sections and 8 reported donor labels to the image members; a directory listing alone does not verify the study.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Package join", "depth": "public repository metadata; retained central-directory evidence", "result": "Current Zenodo file metadata and the earlier 20-image, eight-prefix inventory do not resolve the spatial_list.Rda row-to-image join." } ] } }, { "id": "cand-peng-kadara-2025", "label": "Peng et al. 2026", "title": "Multimodal Spatial-Omics Reveal Co-Evolution of Alveolar Progenitors and Proinflammatory Niches in Progression of Lung Precursor Lesions", "citation": { "authors": "Peng F, et al.", "title": "Multimodal spatial-omics reveal co-evolution of alveolar progenitors and proinflammatory niches in progression of lung precursor lesions", "journal": "Cancer Cell", "year": 2026, "doi": "10.1016/j.ccell.2025.10.004", "url": "https://doi.org/10.1016/j.ccell.2025.10.004" }, "cancers": [ "LUAD" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE307534", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://doi.org/10.1016/j.ccell.2025.10.004" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE307534" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "56 archive previews; CytAssist TIFF is instrument image", "molecular_finding": "All 56 exact; 30 invasive/MIA, 25 AAH/AIS, one normal by titles", "next_step": "Only the 30 invasive or minimally invasive sections are tumour; 25 precursor lesions and one normal stay separate; repeated sections of a patient stay linked.", "sections_listed": 56, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-chen-liu-2024", "label": "Luo et al. 2024", "title": "Single-cell and spatial transcriptome characterize coinhibitory cell-cell communications during histological progression of lung adenocarcinoma", "citation": { "authors": "Luo J, et al.", "title": "Single-cell and spatial transcriptome characterize coinhibitory cell-cell communications during histological progression of lung adenocarcinoma", "journal": "Frontiers in Immunology", "year": 2024, "doi": "10.3389/fimmu.2024.1430163", "url": "https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1430163/full" }, "cancers": [ "LUAD" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "Zenodo 13337961", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1430163/full" ], [ "Data record", "https://zenodo.org/records/13337961" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "Two 2,000 px previews and 3,000 px CytAssist/technical TIFFs", "molecular_finding": "Both complete RAR matrix/spatial packages exact", "next_step": "Original pathology scans and the image transform; the donor relation of the solid and lepidic sections is unknown.", "sections_listed": 2, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-knuch-2026", "label": "Defining the cellular and molecular identities of histologic subtypes in lung adenocarcinoma", "title": "Defining the cellular and molecular identities of histologic subtypes in lung adenocarcinoma", "citation": { "authors": null, "title": "Defining the cellular and molecular identities of histologic subtypes in lung adenocarcinoma", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12853583/" }, "cancers": [ "LUAD" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "release-unresolved" ], "accession": "KAP241022", "access": { "category": "unresolved", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12853583/" ], [ "Data record", "https://kbds.re.kr/KRA" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "public listing or archive inventoried", "states": [ "public-download", "local-qc" ], "image_finding": "Primary full text supplies KAP241022 and CELLxGENE/public code alternatives", "molecular_finding": "GitHub tree is analysis code, not original image release", "next_step": "Inspect the actual spatial subset; do not equate 18 scRNA donors with one source-described Visium specimen.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "outcome": "spatial-release-unresolved", "depth": "primary XML, public CELLxGENE collection API and source repository tree", "findings": "The accession is KAP241022. The linked CELLxGENE collection holds one single-cell dataset of 117,266 cells, not a measured spatial package.", "next_step": "Locate the released spatial subset and its matched H&E separately from the single-cell data.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-deng-micropapillary-2025", "label": "Deng et al. 2025", "title": "Spatial transcriptomics uncovers immune-cell plasticity and dedifferentiation signatures in aggressive lung adenocarcinoma subtypes", "citation": { "authors": "Deng H, et al.", "title": "Spatial transcriptomics uncovers immune-cell plasticity and dedifferentiation signatures in aggressive lung adenocarcinoma subtypes", "journal": "Frontiers in Immunology", "year": 2025, "doi": "10.3389/fimmu.2025.1620886", "url": "https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2025.1620886/full" }, "cancers": [ "LUAD" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "request" ], "accession": null, "access": { "category": "request", "route": null, "links": [ [ "Publication", "https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2025.1620886/full" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "author-release", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Publication route inspected; no actionable matched package", "molecular_finding": "Unverified", "next_step": "Locate release or later ask for processed/original-image package; histology stratum explicit.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-lu-cell-discovery-2023", "label": "Wang et al. 2023", "title": "Spatial transcriptomics delineates molecular features and cellular plasticity in lung adenocarcinoma progression", "citation": { "authors": "Wang Y, et al.", "title": "Spatial transcriptomics delineates molecular features and cellular plasticity in lung adenocarcinoma progression", "journal": "Cell Discovery", "year": 2023, "doi": "10.1038/s41421-023-00591-7", "url": "https://www.nature.com/articles/s41421-023-00591-7" }, "cancers": [ "LUAD" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled" ], "accession": "HRA001238", "access": { "category": "controlled", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41421-023-00591-7" ], [ "Data record", "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA001238" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "access-dependent", "depth": "access boundary reached", "states": [ "dac-approval" ], "image_finding": "HRA001238/raw and primary source links", "molecular_finding": "No controlled package accessed", "next_step": "Locate public processed original-image alternative or formal access route.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-10x-post-xenium-hd", "label": "Visium HD CytAssist Gene Expression Human Lung Cancer post-Xenium experiment", "title": "Visium HD CytAssist Gene Expression Human Lung Cancer post-Xenium experiment", "citation": { "authors": null, "title": "Visium HD CytAssist Gene Expression Human Lung Cancer post-Xenium experiment", "journal": null, "year": null, "doi": null, "url": "https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt" }, "cancers": [ "LUAD" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium HD" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "pathology-review" ], "accession": null, "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "vendor-boundary", "depth": "source or metadata only", "states": [ "vendor-terms" ], "image_finding": "Official vendor source behind registration and terms", "molecular_finding": "No approved downloaded package", "next_step": "Treat vendor form/terms as distinct dependency; do not count post-Xenium assay as independent donor.", "sections_listed": null, "study_local_donors": null } }, { "id": "cand-meti-luad14c", "label": "METI lung adenocarcinoma sample LUAD-14C", "title": "METI lung adenocarcinoma sample LUAD-14C", "citation": { "authors": null, "title": "METI lung adenocarcinoma sample LUAD-14C", "journal": null, "year": null, "doi": null, "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE246011" }, "cancers": [ "LUAD" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located" ], "accession": "GSM8775962/GSE246011", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE246011" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM8775962" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "coordinate-gap", "depth": "components inspected; join incomplete", "states": [ "author-release", "local-qc" ], "image_finding": "Released TIFF is only 2,000 × 1,927", "molecular_finding": "Counts exist but no separate spot-coordinate file listed", "next_step": "Inspect the metadata CSV for coordinates and an original-image or scale route; the released image is not an original scan.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "outcome": "coordinate-gap", "depth": "complete 3360-row metadata CSV", "findings": "The 3,360-row metadata CSV holds barcodes and QC metrics, with no spatial coordinates.", "next_step": "Find the spot-coordinate table and a source-backed image scale; QC metrics are not coordinates.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-simkin2026-gse268014-hd", "label": "Simkin et al. 2026", "title": "Visium HD sections from Simkin et al. 2026", "citation": { "authors": "Simkin D, et al.", "title": "Spatial analysis of head and neck cancer identifies two ecosystems with distinct modes of epithelial-to-mesenchymal transition", "journal": "Nature Genetics", "year": 2026, "doi": "10.1038/s41588-026-02723-7", "url": "https://www.nature.com/articles/s41588-026-02723-7" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium HD" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "identity" ], "accession": "GSE268014", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41588-026-02723-7" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE268014" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "public listing or archive inventoried", "states": [ "public-download", "local-qc" ], "image_finding": "Two source-listed HD specimens P5684/P5624; originals/Parquet listed", "molecular_finding": "26 standard Visium packages inspected; all raw barcodes map, but those overlap existing resource; HD itself not yet fully checked", "next_step": "Audit only GSM9701483/84 HD components; link to existing two patients, add zero new patients; resolve study-versus-assay resource counting.", "sections_listed": null, "study_local_donors": 0 }, "derived_from": [ "simkin-2026" ], "notes": [ "HD re-assays of the existing Simkin patients P5684 and P5624; they add no patients" ], "followup_review": { "date": "2026-10-16", "outcome": "image-alias-review", "depth": "both public HD barcode vectors/Parquet coordinates/scalefactors downloaded", "findings": "Both Visium HD barcode sets match their in-tissue positions exactly (169,359 and 166,335). In each sample, the main TIFF and the brightfield file names carry opposite patient labels (P5684, P5624). The re-assays add no patients.", "next_step": "Confirm the matrix, image, transform and source labels before listing HD sections; keep the source labels and the existing patients.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-arora2023-gse208253", "label": "Arora et al. 2023", "title": "Spatial transcriptomics reveals distinct and conserved tumor core and edge architectures that predict survival and targeted therapy response", "citation": { "authors": "Arora R, et al.", "title": "Spatial transcriptomics reveals distinct and conserved tumor core and edge architectures that predict survival and targeted therapy response", "journal": "Nature Communications", "year": 2023, "doi": "10.1038/s41467-023-40271-4", "url": "https://www.nature.com/articles/s41467-023-40271-4" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE208253", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.nature.com/articles/s41467-023-40271-4" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208253" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "12 previews", "molecular_finding": "All 12 exact", "next_step": "Patient IDs, treatment and original scans.", "sections_listed": 12, "study_local_donors": null }, "reported": [ [ 12, "spatial samples", "primary paper Results" ], [ 10, "unique patients", "primary paper Results" ] ], "followup_review": { "date": "2026-10-16", "outcome": "preview-clinical-correction", "depth": "primary Results and GEO section metadata; supplementary data workbook inspected", "findings": "The primary paper reports 12 spatial samples from 10 unique patients; GEO does not give the sample-to-patient join.", "next_step": "Find the sample-to-patient join; until then the 12 records keep no patient ID, and the 10 patients are reported for the study only.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-cheng2022-gse181300", "label": "Snail-regulated exosomal microRNA-21 suppresses NLRP3 inflammasome activity to enhance cisplatin resistance", "title": "Snail-regulated exosomal microRNA-21 suppresses NLRP3 inflammasome activity to enhance cisplatin resistance", "citation": { "authors": null, "title": "Snail-regulated exosomal microRNA-21 suppresses NLRP3 inflammasome activity to enhance cisplatin resistance", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9413180/" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE181300", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC9413180/" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE181300" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "Eight previews", "molecular_finding": "All eight exact", "next_step": "Original scans and treatment; repeated invasive-front and inner sections of two patients.", "sections_listed": 8, "study_local_donors": 2 }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-gse281978-hpv2024", "label": "Deciphering head and neck cancer microenvironment: Single-cell and spatial transcriptomics reveals HPV-associated differences", "title": "Deciphering head and neck cancer microenvironment: Single-cell and spatial transcriptomics reveals HPV-associated differences", "citation": { "authors": null, "title": "Deciphering head and neck cancer microenvironment: Single-cell and spatial transcriptomics reveals HPV-associated differences", "journal": null, "year": null, "doi": null, "url": "https://pubmed.ncbi.nlm.nih.gov/38235919/" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "image-qc", "calibration" ], "accession": "GSE281978", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pubmed.ncbi.nlm.nih.gov/38235919/" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE281978" ], [ "Original images (Zenodo 15226540)", "https://zenodo.org/records/15226540" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "primary-tumour", "metastatic-tumour" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "Six previews", "molecular_finding": "All six exact", "next_step": "Donor and site join before counting the three paired donors; the PT and LNMT labels conflict with the primary-tissue metadata.", "sections_listed": 6, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "outcome": "original-ready", "depth": "six direct microscopy TIFF byte-range headers; exact source labels; prior molecular checks; coordinate/preview-scale consistency", "findings": "Zenodo 15226540 holds six original RGB OME-TIFFs whose names match the six GEO section titles. Coordinates fit the originals, the supplied scales reproduce the preview dimensions, and the headers give 0.287545 µm per pixel. Three sections are primary tumour and three are nodal metastases.", "next_step": "Join the sections to their donors; registration, calibration accuracy and pathology QC remain open.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-beyaert2025-gse289908", "label": "Spatial Transcriptomic Analysis of Surgical Resection Specimens of Primary Head and Neck Squamous Cell Carcinoma Treated with Afatinib in a Window-of-Opportunity Study (EORTC 90111-24111)", "title": "Spatial Transcriptomic Analysis of Surgical Resection Specimens of Primary Head and Neck Squamous Cell Carcinoma Treated with Afatinib in a Window-of-Opportunity Study (EORTC 90111-24111)", "citation": { "authors": null, "title": "Spatial Transcriptomic Analysis of Surgical Resection Specimens of Primary Head and Neck Squamous Cell Carcinoma Treated with Afatinib in a Window-of-Opportunity Study (EORTC 90111-24111)", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11898532/" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "treated", "calibration" ], "accession": "GSE289908", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11898532/" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE289908" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "coordinate-gap", "depth": "components inspected; join incomplete", "states": [ "author-release", "local-qc" ], "image_finding": "Original-image candidates plus Loupe alignment JSON listed", "molecular_finding": "Three treated (afatinib) matrices; JSON oligo spots have array/image coordinates but no barcode IDs", "next_step": "Recover validated barcode-to-grid/JSON map and original-image relation; no direct expression-coordinate verification yet.", "sections_listed": null, "study_local_donors": 3 }, "followup_review": { "date": "2026-10-16", "outcome": "barcode-grid-gap", "depth": "all three deposited JSON alignment files and barcode vectors inspected", "findings": "Each of the three alignment JSON files lists 4,992 grid and image positions without barcode identifiers; the filtered matrices have 1,340, 2,913 and 1,552 barcodes.", "next_step": "Find a source-backed barcode-to-grid map and validate the transformed positions.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-gessain2024-e-mtab-14409", "label": "TREM2-Expressing Multinucleated Giant Macrophages Are a Biomarker of Good Prognosis in Head and Neck Squamous Cell Carcinoma", "title": "TREM2-Expressing Multinucleated Giant Macrophages Are a Biomarker of Good Prognosis in Head and Neck Squamous Cell Carcinoma", "citation": { "authors": null, "title": "TREM2-Expressing Multinucleated Giant Macrophages Are a Biomarker of Good Prognosis in Head and Neck Squamous Cell Carcinoma", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11609822/" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled" ], "accession": "E-MTAB-14409", "access": { "category": "open", "route": "Public processed .cloupe files in E-MTAB-14409; sharing of the original institutional whole-slide images needs a separate agreement", "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11609822/" ], [ "Data record", "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-14409" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "bounded-public-work", "depth": "public listing or archive inventoried", "states": [ "public-download", "local-qc" ], "image_finding": "Public processed ArrayExpress listing, not globally controlled; original institutional WSI sharing restricted", "molecular_finding": "11 .cloupe files listed, nine patient prefixes; magic inspected, not numerically decoded", "next_step": "Decode the counts, positions and preview inside the .cloupe files; transfer of the original whole-slide images needs a separate agreement.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "outcome": "public-processed-decoding-gap", "depth": "1024-byte cloupe header and 9500-byte index decoded to 65362-byte JSON", "findings": "One .cloupe file's header and index were decoded: 17,945 features, 3,346 barcodes, a spatial projection of each barcode and an embedded 7,572 × 7,626 brightfield image. The numeric blocks and image tiles are not decoded, and the projection scale is not a scanner calibration.", "next_step": "Decode and count-check the expression and spatial blocks and the embedded image transform; transfer of the original whole-slide images needs a separate agreement.", "states": [ "public-download", "local-qc" ], "checks": [] } }, { "id": "cand-frontiers2026-zenodo18238293", "label": "Weeramange et al. 2026", "title": "Spatial transcriptomics and histopathological analyses reveal potential biomarkers and immune features linked to recurrence in head and neck cancer", "citation": { "authors": "Weeramange CE, et al.", "title": "Spatial transcriptomics and histopathological analyses reveal potential biomarkers and immune features linked to recurrence in head and neck cancer", "journal": "Frontiers in Immunology", "year": 2026, "doi": "10.3389/fimmu.2026.1713732", "url": "https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2026.1713732/full" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "verified", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "identity", "image-qc", "calibration" ], "accession": "Zenodo 18238293", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2026.1713732/full" ], [ "Data record", "https://zenodo.org/records/18238293" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "original-ready", "depth": "downloaded components checked", "states": [ "public-download", "local-qc" ], "image_finding": "Four original TIFFs around 10,000 px", "molecular_finding": "Four VisiumV2 centroid sets cover all 13,611 expression-cell-map labels; count-layer sizes match", "next_step": "Treatment and timing; 11 tissue blocks from ten donors share four array areas, and the recurrence field is a later outcome.", "sections_listed": 11, "study_local_donors": 10 }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original level and calibration", "depth": "bounded public image header/range and coordinate checks; retained complete-image checks reused where available", "result": "Original level kept. Pixel sizes read from image headers and frame checks are recorded on the sections where available; registration and calibration accuracy are not signed off." } ] } }, { "id": "cand-causer2023-uq", "label": "Deep spatial-omics analysis of Head & Neck carcinomas provides alternative therapeutic targets and rationale for treatment failure", "title": "Deep spatial-omics analysis of Head & Neck carcinomas provides alternative therapeutic targets and rationale for treatment failure", "citation": { "authors": null, "title": "Deep spatial-omics analysis of Head & Neck carcinomas provides alternative therapeutic targets and rationale for treatment failure", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10499928/" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "pathology-review" ], "accession": "UQ eSpace DOI 10.48610/698bb9e", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10499928/" ], [ "Data record", "https://doi.org/10.48610/698bb9e" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "technical-gap", "depth": "public download failed", "states": [ "download-failure" ], "image_finding": "Primary article says public processed Visium/PhenoCycler at UQ DOI; direct source 403", "molecular_finding": "GSE181919 is related scRNA, not substitute spatial package", "next_step": "Retrieve exact UQ processed spatial package and assayed-section H&E; separate PhenoCycler and controlled raw reads.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public route retry", "depth": "primary XML, public repository tree and two failed public landing retries", "result": "The UQ DOI and landing page return HTTP 403, a technical gap; the paper states that processed Visium and PhenoCycler data are public and raw reads restricted." } ] } }, { "id": "cand-li2024-hra005551-hra005576", "label": "Cancer-associated fibroblast subsets in head and neck squamous cell carcinoma", "title": "Cancer-associated fibroblast subsets in head and neck squamous cell carcinoma", "citation": { "authors": null, "title": "Cancer-associated fibroblast subsets in head and neck squamous cell carcinoma", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10790129/" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Spatial RNA (protocol unverified)" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled" ], "accession": "HRA005551; HRA005576", "access": { "category": "controlled", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10790129/" ], [ "Data record", "https://ngdc.cncb.ac.cn/gsa-human/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "access-dependent", "depth": "access boundary reached", "states": [ "dac-approval" ], "image_finding": "Primary paper says nonprofit research can be approved; accession typo HRA0005576 corrected to HRA005576", "molecular_finding": "No controlled package accessed", "next_step": "Processed public alternative or formal approval.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "primary availability XML read", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-hypopharynx2025-ccrt", "label": "Hypopharyngeal cancer chemoradiotherapy resistance, spatial transcriptomics", "title": "Hypopharyngeal cancer chemoradiotherapy resistance, spatial transcriptomics", "citation": { "authors": null, "title": "Hypopharyngeal cancer chemoradiotherapy resistance, spatial transcriptomics", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12748936/" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "request" ], "accession": null, "access": { "category": "request", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12748936/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "author-release", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Paper explicitly restricts public sharing for privacy/ethics", "molecular_finding": "No public package", "next_step": "Author/institution release needed for processed RNA/image/clinical map.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Public processed alternative", "depth": "primary availability XML read", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cand-gse301720-ici2026", "label": "Head and neck squamous cell carcinoma immune-checkpoint inhibitor spatial study", "title": "Head and neck squamous cell carcinoma immune-checkpoint inhibitor spatial study", "citation": { "authors": null, "title": "Head and neck squamous cell carcinoma immune-checkpoint inhibitor spatial study", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13093465/" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE301720", "access": { "category": "open", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC13093465/" ], [ "Data record", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE301720" ] ] }, "verification": "file-checked", "verified_on": "2026-10-16", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "preview-ready", "depth": "downloaded components checked", "states": [ "public-download", "author-release", "local-qc" ], "image_finding": "Eight previews", "molecular_finding": "All eight exact", "next_step": "Clinical timing and source site; response labels do not show that samples were taken after immunotherapy.", "sections_listed": 8, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "cand-oraltumorigenesis2025-preprint", "label": "Integrative spatiotemporal analysis of squamous tumorigenesis", "title": "Integrative spatiotemporal analysis of squamous tumorigenesis", "citation": { "authors": null, "title": "Integrative spatiotemporal analysis of squamous tumorigenesis", "journal": null, "year": null, "doi": null, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12621683/" }, "cancers": [ "HNSC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium HD" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "release-unresolved" ], "accession": null, "access": { "category": "unresolved", "route": null, "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12621683/" ] ] }, "verification": "source-described", "verified_on": "2026-10-09", "description": null, "compartments": [ "tumour-unspecified" ], "backlog_review": { "date": "2026-10-16", "outcome": "release-unresolved", "depth": "source or metadata only", "states": [ "author-release" ], "image_finding": "Primary preprint includes human and murine precursor/invasive TMAs", "molecular_finding": "No released source package verified", "next_step": "Identify human invasive subset and accession; exclude mouse/precursor counts from invasive HNSC denominator.", "sections_listed": null, "study_local_donors": null }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Release search", "depth": "bounded Europe PMC title search", "result": "A bounded literature search found no measured spatial package with original images; other routes may still need review." }, { "check": "Public processed alternative", "depth": "bounded primary metadata/availability retrieval; incomplete availability coverage", "result": "No qualified public processed or image alternative found; declared access restrictions apply only to those files, and retrieval failures are technical gaps." } ] } }, { "id": "cscc-10x-ffpe", "label": "10x Genomics cervical SCC, Visium FFPE", "title": "10x Human Cervical Cancer FFPE", "citation": null, "cancers": [ "CESC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "listed-together", "gates": [ "he-unverified", "identity", "treatment-review" ], "accession": "10x Genomics dataset; block C00084155.1a", "access": { "category": "account", "route": "Vendor dataset page; downloading requires registration and acceptance of the vendor's terms (CC BY 4.0 data). No registration was made.", "links": [ [ "Vendor dataset", "https://www.10xgenomics.com/datasets/human-cervical-cancer-1-standard" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Vendor Visium FFPE demonstration of one invasive cervical squamous cell carcinoma specimen, reported as T1bN0M0, stage IB (block C00084155.1a). The source describes a 20x H&E of the assayed section; the original image file and its registration were not checked here.", "compartments": [ "primary-tumour" ], "reported": [ [ 1, "section (vendor specimen)", "vendor dataset page" ] ], "notes": [ "Treatment and donor provenance", "Obtain original H&E, count matrix, coordinates, scale factors and verify overlay", "Also redistributed through HEST TENX50; not a separate cohort.", "Vendor download requires registration and acceptance of terms; no form was submitted" ], "spatial_review": { "id": "cscc-10x-ffpe", "date": "2026-10-15", "analysis_cohort": "CSCC", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium FFPE", "role": "candidate resource", "image_status": "Source describes 20x H&E; full-resolution metadata 13761x12701 in HEST v1.1; original file download/registration not independently checked", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "specimen": "human clinical cervical invasive SCC T1bN0M0 IB", "block": "C00084155.1a", "reused_in": [ "HEST TENX50" ], "route_review": { "date": "2026-10-15", "status": "Vendor page requires registration and terms before download", "states": [ "vendor-terms", "local-qc" ], "next_step": "Complete the vendor registration if wanted (not done), then check the files, H&E and donor history.", "sections_with_matching_coordinates": null } } }, { "id": "cscc-hpv-gse208654", "label": "Guo et al. 2023, HPV progression series", "title": "Spatiotemporally deciphering the mysterious mechanism of persistent HPV-induced malignant transition and immune remodelling from HPV-infected normal cervix, precancer to cervical cancer: Integrating single-cell RNA-sequencing and spatial transcriptome", "citation": { "authors": "Guo C, et al.", "title": "Spatiotemporally deciphering the mysterious mechanism of persistent HPV-induced malignant transition and immune remodelling from HPV-infected normal cervix, precancer to cervical cancer: Integrating single-cell RNA-sequencing and spatial transcriptome", "journal": "Clinical and Translational Medicine", "year": 2023, "doi": "10.1002/ctm2.1219", "url": "https://doi.org/10.1002/ctm2.1219" }, "cancers": [ "CESC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Spatial transcriptomics array (platform to confirm)" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "coordinates", "calibration", "identity" ], "accession": "GSE208654 (SCC section GSM6360691)", "access": { "category": "open", "route": "public processed GEO", "links": [ [ "GEO series", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208654" ], [ "Full text (PMC)", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10040725/" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Four spatial sections along cervical HPV progression: one squamous cell carcinoma (GSM6360691), one adenocarcinoma (GSM6360692), one HPV-positive normal cervix and one HSIL. Only the carcinoma section of squamous histology belongs to the CSCC scope; the others are kept separate. For GSM6360691 the deposited H&E (10,322 × 9,666 pixels) and expression for 1,757 spots were retrieved, and processing and image evidence support Visium, but no released spot coordinates or scale factors were found, so it is not yet a complete spatial package.", "compartments": [ "primary-tumour", "normal", "precursor" ], "reported": [ [ 1, "squamous cell carcinoma section (GSM6360691)", "GEO series", "CESC" ], [ 1, "adenocarcinoma section (GSM6360692), outside CSCC", "GEO series" ], [ 2, "HPV-positive normal and HSIL sections", "GEO series" ], [ 4, "sections in the complete series", "GEO series" ] ], "notes": [ "Use GSM6360691 (SCC); exclude GSM6360692 (ADC) from CSCC core", "Keep HPV-positive normal and HSIL separate", "Recover spatial coordinates/scale and original image calibration" ], "spatial_review": { "id": "cscc-hpv-gse208654", "date": "2026-10-15", "analysis_cohort": "CSCC", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium, supported by processing and image evidence", "role": "candidate resource", "image_status": "GSM6360691 H&E 10,322 × 9,666 pixels and 1,757 expression spots retrieved; coordinates and scale factors not released", "treatment_status": "GEO treatment: NO; crosswalk and specimen history still require review", "treatment_class": "reported-untreated", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": { "sample_ids": [ "GSM6360691" ], "exclude_sample_ids": [ "GSM6360692" ], "normal_or_precursor_ids": [ "GSM6360689", "GSM6360690" ] }, "route_review": { "date": "2026-10-15", "status": "H&E and expression retrieved; spot coordinates missing", "states": [ "public-download", "author-release", "local-qc" ], "next_step": "Ask the submitter for the tissue-position table and scale factors of GSM6360691, the image calibration and the clinical provenance.", "sections_with_matching_coordinates": null } } }, { "id": "cscc-ou-stereo", "label": "Ou et al. 2022", "title": "Single-Nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell Carcinoma", "citation": { "authors": "Ou Z, et al.", "title": "Single-Nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell Carcinoma", "journal": "Advanced Science", "year": 2022, "doi": "10.1002/advs.202203040", "url": "https://doi.org/10.1002/advs.202203040" }, "cancers": [ "CESC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Stereo-seq" ], "preservation": [ "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "serial-section", "gates": [ "serial-section", "release-unresolved", "he-not-located", "treatment-review" ], "accession": "CNSA CNP0002543", "access": { "category": "unresolved", "route": "CNSA CNP0002543 listed in the paper; the public listing did not resolve", "links": [ [ "Publication", "https://doi.org/10.1002/advs.202203040" ], [ "Full text (PMC)", "https://pmc.ncbi.nlm.nih.gov/articles/PMC9561780/" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Stereo-seq study of cervical squamous cell carcinoma reporting 14 tumour patients on 15 slides and two normal-tissue patients on three slides, alongside single-nucleus RNA-seq. H&E comes from serial cryosections, not from the assayed section. The data are listed under CNSA CNP0002543, but the project listing did not resolve and the CNSA accession search returned no result; this does not establish controlled access.", "compartments": [ "tumour-unspecified", "normal" ], "reported": [ [ 14, "tumour patients", "publication" ], [ 15, "tumour slides", "publication" ], [ 2, "normal-tissue patients", "publication" ], [ 3, "normal-tissue slides", "publication" ] ], "notes": [ "Retrieve CNP0002543 and original scans/section crosswalk", "Preserve serial-section linkage", "Review treatment, primary site and image registration" ], "spatial_review": { "id": "cscc-ou-stereo", "date": "2026-10-15", "analysis_cohort": "CSCC", "assay_classes": [ "whole-transcriptome" ], "platform": "Stereo-seq", "role": "candidate resource", "image_status": "H&E from serial cryosections; not exact same-section H&E", "treatment_status": "not established in this review", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "route_review": { "date": "2026-10-15", "status": "Serial-section study; public data route unresolved", "states": [ "download-failure", "author-release" ], "next_step": "Ask the authors or CNSA support for a working route to CNP0002543, processed matrices and coordinates, and original serial H&E with patient and section mapping.", "sections_with_matching_coordinates": null } } }, { "id": "escc-hra000776-omix009524", "label": "HRA000776 / OMIX009524, multistage ESCC", "title": "Multistage ESCC spatial profiling with linked image deposit", "citation": { "authors": null, "title": "Multistage ESCC spatial profiling with linked image deposit", "journal": "NGDC GSA-Human", "year": null, "doi": null, "url": "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA000776" }, "cancers": [ "ESCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium (library details to verify)" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "controlled", "he-unverified", "identity" ], "accession": "HRA000776; OMIX009524", "access": { "category": "controlled", "route": "controlled HRA000776 and OMIX009524; no approval obtained", "links": [ [ "GSA-Human", "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA000776" ], [ "Image release", "https://ngdc.cncb.ac.cn/omix/release/OMIX009524" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Controlled multistage ESCC spatial profiling (HRA000776) with a linked image deposit (OMIX009524) that provides Space Ranger hires images for five named tumours (LZE7T, LZE8T, LZE21T, LZE22T and LZE24T). These are processed images, not verified original-resolution scans. The parent HRA000776 cohort is described as treatment-naive, but the spatial subset's link to it is not established, and the parent cohort's patient count must not be transferred. A live refresh of the access page timed out; the controlled-access policy recorded earlier is kept. No access has been requested or approved.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 5, "named tumour image packages", "OMIX009524 release" ] ], "notes": [ "Request controlled data only through normal access route", "Do not call Space Ranger hires original-resolution", "Review basaloid SCC metadata and donor/sample crosswalk" ], "spatial_review": { "id": "escc-hra000776-omix009524", "date": "2026-10-15", "analysis_cohort": "ESCC", "assay_classes": [ "whole-transcriptome" ], "platform": "10x spatial; verify library details", "role": "candidate resource", "image_status": "OMIX009524 provides Space Ranger hires images for five named tumours; original-resolution images not established", "treatment_status": "parent cohort described as treatment-naive; spatial subset linkage not established", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": { "sample_ids": [ "LZE7T", "LZE8T", "LZE21T", "LZE22T", "LZE24T" ] }, "route_review": { "date": "2026-10-15", "status": "Controlled data; image and assay crosswalk unresolved", "states": [ "dac-approval", "author-release", "local-qc" ], "next_step": "Apply through the repository's data access committee only if the data are needed, and ask for the five-tumour image and assay crosswalk and original scans.", "sections_with_matching_coordinates": null } } }, { "id": "escc-hra007162", "label": "HRA007162, ESCC single-cell and spatial", "title": "Single-cell and spatial multi-omics of human ESCC", "citation": { "authors": null, "title": "Single-cell and spatial multi-omics of human ESCC", "journal": "NGDC GSA-Human", "year": null, "doi": null, "url": "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA007162" }, "cancers": [ "ESCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "package-unverified", "he-not-located", "identity" ], "accession": "HRA007162", "access": { "category": "open", "route": "Open raw reads at GSA-Human; processed spatial matrix, original H&E and coordinates not released", "links": [ [ "GSA-Human", "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA007162" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Single-cell and spatial multi-omics study of ESCC with Visium data reported for five cancer tissues. NGDC lists the raw reads as open access: the public directory has 13 run folders, and experiment HRX1389699 uses Visium. The earlier controlled-access label was wrong. A processed spatial matrix, original H&E and coordinates were not found, and open raw reads alone do not supply them. Possible overlap with HRA000776 must be resolved before any aggregation.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 5, "cancer tissues", "archive description" ] ], "notes": [ "Verify archive contents, original images and processed matrices", "Resolve possible overlap with HRA000776 before aggregating", "Open raw reads: do not inherit the controlled status of HRA000776 or HRA003627" ], "spatial_review": { "id": "escc-hra007162", "date": "2026-10-15", "analysis_cohort": "ESCC", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium, source-described", "role": "candidate resource", "image_status": "Original H&E, processed matrix and coordinates not released", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "route_review": { "date": "2026-10-15", "status": "Open raw reads; processed and image package unresolved", "states": [ "public-download", "author-release", "local-qc" ], "next_step": "Ask the study authors for the processed five-case spatial package, original H&E, coordinates and a de-identified donor and run crosswalk.", "sections_with_matching_coordinates": null } } }, { "id": "escc-precancer-geomx", "label": "Liu et al. 2023, GeoMx precancer", "title": "Spatial transcriptomics analysis of esophageal squamous precancerous lesions and their progression to esophageal cancer", "citation": { "authors": "Liu X, et al.", "title": "Spatial transcriptomics analysis of esophageal squamous precancerous lesions and their progression to esophageal cancer", "journal": "Nature Communications", "year": 2023, "doi": "10.1038/s41467-023-40343-5", "url": "https://doi.org/10.1038/s41467-023-40343-5" }, "cancers": [ "ESCA" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "GeoMx WTA (ROI)" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "serial-section", "gates": [ "platform", "package-unverified", "serial-section", "identity" ], "accession": null, "access": { "category": "request", "route": "Public source-data workbook (selected genes, 42 ROIs); complete ROI matrices on request; raw reads HRA003627 controlled", "links": [ [ "Publication", "https://doi.org/10.1038/s41467-023-40343-5" ], [ "Source-data workbook", "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-023-40343-5/MediaObjects/41467_2023_40343_MOESM4_ESM.xlsx" ], [ "Author repository", "https://github.com/hrcnlab/escc_pipline" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "GeoMx whole-transcriptome ROI profiling of oesophageal squamous precancerous lesions and cancer in 19 patients: six with low-grade and six with high-grade intraepithelial neoplasia, and seven with invasive ESCC; normal regions come from the low-grade donors. Forty-two ROIs were profiled, with H&E from serial sections. The public source-data workbook gives selected genes for the 42 ROIs, not the complete whole-transcriptome matrix, and the author repository holds analysis scripts only; raw reads (HRA003627) are controlled. ROI data are a supplementary resource, kept apart from spot- or bin-based transcriptomics.", "compartments": [ "precursor", "tumour-unspecified" ], "reported": [ [ 7, "patients with invasive ESCC", "publication", "ESCA" ], [ 19, "patients in the study", "publication" ], [ 12, "patients with intraepithelial neoplasia (six low-grade, six high-grade)", "publication" ], [ 42, "ROIs", "publication" ] ], "notes": [ "Keep ROI data separate from spot/bin-based transcriptomics", "Seven invasive ESCC patients within a 19-patient study; normal regions share the low-grade donors", "The public workbook is a selected gene set, not the complete whole-transcriptome matrix" ], "spatial_review": { "id": "escc-precancer-geomx", "date": "2026-10-15", "analysis_cohort": "ESCC", "assay_classes": [ "roi" ], "platform": "GeoMx WTA ROI profiling", "role": "supplementary ROI resource", "image_status": "Serial-section H&E; ROI geometries and image crosswalk not released", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "route_review": { "date": "2026-10-15", "status": "Selected genes public; complete ROI matrix not released", "states": [ "author-release", "local-qc" ], "next_step": "Ask the corresponding authors for the complete normalised and raw ROI matrices, QC annotations, ROI geometries and the serial H&E crosswalk.", "sections_with_matching_coordinates": null } } }, { "id": "kirc-meylan-gse175540", "label": "Meylan et al. 2022", "title": "Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer", "citation": { "authors": "Meylan M, et al.", "title": "Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer", "journal": "Immunity", "year": 2022, "doi": "10.1016/j.immuni.2022.02.001", "url": "https://doi.org/10.1016/j.immuni.2022.02.001" }, "cancers": [ "KIRC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE", "Visium" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "linkage": "listed-together", "gates": [ "he-not-located", "identity", "image-qc", "calibration" ], "accession": "GSE175540", "access": { "category": "open", "route": "public processed data; raw reads withheld for privacy", "links": [ [ "GEO series", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175540" ], [ "Publication", "https://doi.org/10.1016/j.immuni.2022.02.001" ], [ "STOmicsDB mirror", "https://db.cngb.org/stomics/datasets/STDS0000223/data" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Visium data from 24 primary ccRCC tumours (12 FFPE, 12 fresh frozen) in a study of tertiary lymphoid structures; the primary paper documents treatment-naive primary ccRCC. Processed data are public and raw reads are withheld. All 24 deposited section packages have expression barcodes that match their tissue coordinates exactly, but the images are previews of at most 2,000 pixels; a check of all 426 links of the STOmicsDB mirror found 48 preview PNGs and no original scan. The public clinical Table S1 could not be downloaded (a technical failure), so the donor, section and grade join is unresolved.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 24, "spatial samples", "GEO series" ], [ 12, "FFPE samples", "GEO series" ], [ 12, "fresh-frozen samples", "GEO series" ] ], "notes": [ "Recover original scans and patient/section crosswalk", "Do not treat 24 HEST donor labels as independent verified patients", "Also redistributed through HEST INT1-INT24 (verify exact IDs in retained metadata); not a separate cohort.", "Review TLS enrichment", "Study-level treatment-naive status is documented in the primary paper", "Clinical Table S1 is publicly linked but its download failed: a technical gap, not author-only data", "Matched data with preview image: 24 checked section packages, not yet listed as individual section records" ], "spatial_review": { "id": "kirc-meylan-gse175540", "date": "2026-10-15", "analysis_cohort": "KIRC", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium FFPE and fresh frozen", "role": "candidate resource", "image_status": "All 24 section packages checked: exact barcode-coordinate agreement; previews of at most 2,000 pixels; no TIFF, SVS or NDPI among 426 mirror links", "treatment_status": "treatment-naive primary ccRCC documented in the primary paper", "treatment_class": "reported-untreated", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "reused_in": [ "HEST INT1-INT24 (verify exact IDs in retained metadata)" ], "route_review": { "date": "2026-10-15", "status": "24 section packages checked; preview images only", "states": [ "public-download", "download-failure", "author-release", "local-qc" ], "next_step": "Retry the public clinical table, then ask the submitter for the original H&E of the 24 sections and the donor, section and grade crosswalk.", "sections_with_matching_coordinates": 24 } }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "kirc-egad00001008781", "label": "Li et al. 2022, ccRCC Visium (EGAD00001008781)", "title": "Understanding multicellular dynamics of ccRCC", "citation": { "authors": "Li R, et al.", "title": "Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer", "journal": "Cancer Cell", "year": 2022, "doi": "10.1016/j.ccell.2022.11.001", "url": "https://doi.org/10.1016/j.ccell.2022.11.001" }, "cancers": [ "KIRC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "he-not-located", "calibration", "image-qc" ], "accession": "EGAD00001008781 (EGAS00001006045)", "access": { "category": "open", "route": "Public processed H5AD files: Mendeley Data g67bkbnhhg.1 and the Sanger public FTP directory ftp.sanger.ac.uk/pub/teams/332/mapping_single_cell_RCC (anonymous FTP works; the Mendeley file link returned an error). Controlled raw CRAMs at EGA are optional for processed reuse.", "links": [ [ "EGA dataset", "https://ega-archive.org/datasets/EGAD00001008781" ], [ "Publication", "https://doi.org/10.1016/j.ccell.2022.11.001" ], [ "Mendeley Data", "https://data.mendeley.com/datasets/g67bkbnhhg/1" ], [ "Project page", "https://www.sanger.ac.uk/project/microenvironment-of-kidney-cancer/" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Visium study of clear-cell RCC: 16 sections from eight ccRCC patients (38,836 spots), covering tumour core and the tumour–normal interface. Processed spatial data are public through Mendeley Data (g67bkbnhhg.1) and Sanger's public FTP directory; metadata inspection of both spatial H5AD files confirms the eight patients and 16 sections. Both files copy the image metadata of all 16 sections, so together they hold 16 sections, not 32. Their images are previews (2,000 and 600 pixels). The paper documents treatment-naive surgery. Controlled raw reads (EGAD00001008781) are needed only for raw-data reuse; original H&E and calibration need an author release. Numerical matrix QC has not been done.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 8, "patients with ccRCC", "public H5AD metadata" ], [ 16, "sections", "public H5AD metadata" ], [ 38836, "spots", "public H5AD metadata" ] ], "notes": [ "Retain tumour core versus tumour-normal interface", "The two public H5AD files copy all 16 sections' image metadata: count 16 sections, not 32", "EGA approval is needed only for controlled raw reads", "Original H&E and calibration need an author release" ], "spatial_review": { "id": "kirc-egad00001008781", "date": "2026-10-15", "analysis_cohort": "KIRC", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium", "role": "candidate resource", "image_status": "Public H5AD images are 2,000- and 600-pixel previews; original scans not among the public files", "treatment_status": "treatment-naive surgery documented in the primary paper", "treatment_class": "reported-untreated", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "route_review": { "date": "2026-10-15", "status": "Public processed data located; eight patients and 16 sections confirmed", "states": [ "public-download", "author-release", "local-qc" ], "next_step": "Ask the study team for original H&E and calibration; apply to EGA only if raw reads are needed.", "sections_with_matching_coordinates": null } } }, { "id": "kirc-treated-gse294006", "label": "GSE294006, treated advanced ccRCC", "title": "Treatment-induced hypoxia and resistance in advanced ccRCC", "citation": { "authors": null, "title": "Treatment-induced hypoxia and resistance in advanced ccRCC", "journal": "NCBI GEO", "year": null, "doi": null, "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294006" }, "cancers": [ "KIRC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "listed-together", "gates": [ "treated", "he-not-located", "image-qc", "calibration" ], "accession": "GSE294006", "access": { "category": "open", "route": "public processed GEO", "links": [ [ "GEO series", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294006" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Three primary ccRCC tumours resected after systemic treatment, two of them sarcomatoid, profiled with Visium FFPE. The study concerns advanced disease, but all three samples are primary tumours. Kept outside the untreated reference as an exploratory treated comparison; original-resolution images are still to be checked.", "compartments": [ "primary-tumour" ], "reported": [ [ 3, "primary-tumour samples after systemic treatment", "GEO series" ], [ 3, "donor labels", "GEO series" ] ], "notes": [ "Keep outside untreated primary reference", "Two specimens are sarcomatoid ccRCC", "Advanced-disease study title does not make these metastatic tissue: all GSMs say primary tumour", "Matched data with preview image: 3 checked section packages, not yet listed as individual section records" ], "spatial_review": { "id": "kirc-treated-gse294006", "date": "2026-10-15", "analysis_cohort": "KIRC", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium FFPE", "role": "exploratory treated spatial comparison", "image_status": "All three expression and coordinate sets agree; supplied images at most 2,000 pixels; originals not found", "treatment_status": "all three after systemic treatment", "treatment_class": "treated", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": { "sample_ids": [ "GSM8896252", "GSM8896253", "GSM8896254" ] }, "route_review": { "date": "2026-10-15", "status": "Three section packages checked; preview images only", "states": [ "public-download", "author-release", "local-qc" ], "next_step": "Ask the submitter for original H&E, calibration and matching metadata for the three sections.", "sections_with_matching_coordinates": 3 } }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "kirc-10x-xenium-protein", "label": "10x Genomics ccRCC, Xenium RNA and protein", "title": "FFPE human renal ccRCC, Xenium gene and protein", "citation": { "authors": "10x Genomics", "title": "FFPE human renal ccRCC, Xenium gene and protein", "journal": "10x Genomics datasets", "year": null, "doi": null, "url": "https://www.10xgenomics.com/datasets/xenium-protein-ffpe-human-renal-ccrcc" }, "cancers": [ "KIRC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna", "spatial-protein" ], "techniques": [ "Xenium" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "platform", "he-unverified", "treatment-review" ], "accession": "10x Genomics dataset", "access": { "category": "account", "route": "Vendor dataset page; downloading requires registration and acceptance of the vendor's terms (CC BY 4.0 data). No registration was made.", "links": [ [ "Vendor dataset", "https://www.10xgenomics.com/datasets/xenium-protein-ffpe-human-renal-ccrcc" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Vendor FFPE ccRCC dataset with targeted Xenium RNA (377-gene base panel plus custom genes) and a 27-plex protein panel. Targeted RNA and protein measurements are kept separate from whole-transcriptome resources; H&E availability and alignment were not checked.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 1, "sample (vendor specimen)", "vendor dataset page" ] ], "notes": [ "Verify post-assay H&E and alignment", "Keep targeted RNA/protein separate from broad-transcriptome resource", "Vendor download requires registration and acceptance of terms; no form was submitted" ], "spatial_review": { "id": "kirc-10x-xenium-protein", "date": "2026-10-15", "analysis_cohort": "KIRC", "assay_classes": [ "rna-protein" ], "platform": "Xenium targeted RNA plus 27-plex protein", "role": "targeted supplementary resource", "image_status": "H&E availability/registration not checked", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "panel": "377-gene base panel plus custom genes; 27-plex protein", "route_review": { "date": "2026-10-15", "status": "Vendor page requires registration and terms before download", "states": [ "vendor-terms", "local-qc" ], "next_step": "Complete the vendor registration if wanted (not done), then check the files, H&E and donor history.", "sections_with_matching_coordinates": null } } }, { "id": "kirp-10x-xenium-preview", "label": "10x Genomics kidney preview, Xenium (papillary RCC)", "title": "Human kidney preview data, Xenium multi-tissue and cancer panel", "citation": { "authors": "10x Genomics", "title": "Human kidney preview data, Xenium multi-tissue and cancer panel", "journal": "10x Genomics datasets", "year": null, "doi": null, "url": "https://www.10xgenomics.com/datasets/human-kidney-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard" }, "cancers": [ "KIRP" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Xenium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "listed-together", "gates": [ "platform", "he-unverified", "treatment-review" ], "accession": "10x Genomics dataset", "access": { "category": "account", "route": "Vendor dataset page; downloading requires registration and acceptance of the vendor's terms (CC BY 4.0 data). No registration was made.", "links": [ [ "Vendor dataset", "https://www.10xgenomics.com/datasets/human-kidney-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Vendor Xenium preview with one papillary RCC block and one non-diseased kidney block from two donors, measured with a preliminary 377-gene targeted panel. Post-assay H&E and alignment are described by the source but were not checked here. It is one tumour specimen, not two tumour donors, and no whole-transcriptome papillary RCC package was verified in this review.", "compartments": [ "tumour-unspecified", "normal" ], "reported": [ [ 1, "papillary RCC sample", "vendor dataset page" ], [ 1, "non-diseased kidney sample", "vendor dataset page" ], [ 2, "donors in the dataset", "vendor dataset page" ] ], "notes": [ "Keep one PRCC block separate from non-diseased block", "Do not count two samples as two tumour donors", "Preliminary panel; retain release version", "No broad-transcriptome papillary-RCC package verified in this screen", "Also redistributed through HEST TENX105; not a separate cohort.", "Vendor download requires registration and acceptance of terms; no form was submitted" ], "spatial_review": { "id": "kirp-10x-xenium-preview", "date": "2026-10-15", "analysis_cohort": "KIRP", "assay_classes": [ "targeted-rna" ], "platform": "Xenium targeted RNA, 377 genes", "role": "targeted supplementary resource", "image_status": "Post-Xenium H&E and alignment are explicitly described; files/overlay not independently checked", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "reused_in": [ "HEST TENX105" ], "route_review": { "date": "2026-10-15", "status": "Vendor page requires registration and terms before download", "states": [ "vendor-terms", "local-qc" ], "next_step": "Complete the vendor registration if wanted (not done), then check the files, H&E and donor history.", "sections_with_matching_coordinates": null } } }, { "id": "kirp-macrophage-abstract", "label": "Soupir et al., papillary RCC CosMx study", "title": "Spatial Clustering of Immunosuppressive Macrophages in Papillary Renal Cell Carcinoma", "citation": { "authors": "Soupir A, et al.", "title": "Spatial Clustering of Immunosuppressive Macrophages in Papillary Renal Cell Carcinoma", "journal": "The Oncologist", "year": 2024, "doi": "10.1093/oncolo/oyae181.034", "url": "https://doi.org/10.1093/oncolo/oyae181.034" }, "cancers": [ "KIRP" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna", "spatial-protein" ], "techniques": [ "Multiplex immunofluorescence", "Targeted spatial RNA (960 transcripts)" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "platform", "identity", "he-not-located", "treatment-review" ], "accession": null, "access": { "category": "open", "route": "Public Seurat object (Harvard Dataverse, CC BY 4.0; Zenodo copy); clinical and H&E mapping from the study team", "links": [ [ "Publication", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11301905/" ], [ "Full paper (2025)", "https://doi.org/10.1177/24684562251358595" ], [ "Harvard Dataverse", "https://doi.org/10.7910/DVN/OUWYBU" ], [ "Zenodo copy", "https://zenodo.org/records/12730227" ], [ "Public code", "https://github.com/FridleyLab/ccRCC_CosMx_SMI_2023" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Study of immunosuppressive macrophages in papillary RCC. The 2025 full paper describes a CosMx 960-target RNA assay on tissue from 11 mixed-RCC patients, with four papillary and 24 clear-cell cores across three orthogonal sections; its 16 papillary and 70 clear-cell RCC patients are multiplex-IF cohorts, not spatial RNA counts. A public Seurat object (Harvard Dataverse OUWYBU, CC BY 4.0; also on Zenodo 12730227) holds 199,112 cells and three slide identifiers but no patient, histology or treatment crosswalk, and the broader deposit spans several treatment groups. Both repositories direct clinical enquiries to Brandon Manley, and the public code refers to an unreleased clinical table.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 11, "mixed-RCC patients prepared for spatial RNA", "full paper" ], [ 4, "papillary RCC tissue cores", "full paper" ], [ 24, "clear-cell RCC tissue cores", "full paper" ], [ 3, "orthogonal sections", "full paper" ], [ 16, "papillary RCC patients, multiplex IF (not a spatial RNA count)", "conference abstract" ], [ 70, "clear-cell RCC patients, multiplex IF", "conference abstract" ] ], "notes": [ "16 pRCC is the mIF cohort, not the spatial RNA sample count", "Four papillary cores and 11 mixed-RCC patients do not give a papillary patient count", "Do not apply the paper subset's surgical eligibility to the whole public release", "Clinical crosswalk needed from Brandon Manley, as both repositories state; never request internal record numbers" ], "spatial_review": { "id": "kirp-macrophage-abstract", "date": "2026-10-15", "analysis_cohort": "KIRP", "assay_classes": [ "targeted-rna", "protein-imaging" ], "platform": "CosMx 960-target RNA; multiplex IF in separate cohorts", "role": "candidate resource", "image_status": "Slide identifiers released; H&E mapping and registration not released", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "route_review": { "date": "2026-10-15", "status": "Public molecular object; clinical and H&E crosswalk needed from the study team", "states": [ "public-download", "author-release", "local-qc" ], "next_step": "Ask Brandon Manley, as both repositories direct, for a de-identified slide-to-patient, histology and treatment crosswalk, the paper's subset membership and H&E registration.", "sections_with_matching_coordinates": null } } }, { "id": "lusc-10x-cytassist", "label": "10x Genomics lung SCC, Visium CytAssist FFPE", "title": "Human lung cancer FFPE, squamous cell carcinoma (Visium CytAssist)", "citation": { "authors": "10x Genomics", "title": "Human lung cancer FFPE, squamous cell carcinoma (Visium CytAssist)", "journal": "10x Genomics datasets", "year": null, "doi": null, "url": "https://www.10xgenomics.com/datasets/human-lung-cancer-ffpe-2-standard" }, "cancers": [ "LUSC" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium CytAssist" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "listed-together", "gates": [ "he-unverified", "identity", "treatment-review" ], "accession": "10x Genomics dataset; slide V42A20-354 D1", "access": { "category": "account", "route": "Vendor dataset page; downloading requires registration and acceptance of the vendor's terms (CC BY 4.0 data). No registration was made.", "links": [ [ "Vendor dataset", "https://www.10xgenomics.com/datasets/human-lung-cancer-ffpe-2-standard" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Vendor Visium CytAssist FFPE demonstration of one lung squamous cell carcinoma specimen (slide V42A20-354, area D1). The source describes a 20x Olympus VS200 microscope H&E, distinct from the CytAssist instrument image; its listed size of 35,637 × 29,395 pixels and the transform were not checked here.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 1, "sample (vendor specimen)", "vendor dataset page" ] ], "notes": [ "Keep original microscopy H&E distinct from CytAssist instrument image", "Check donor history and registration", "Also redistributed through HEST TENX62; not a separate cohort.", "Vendor download requires registration and acceptance of terms; no form was submitted" ], "spatial_review": { "id": "lusc-10x-cytassist", "date": "2026-10-15", "analysis_cohort": "LUSC", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium CytAssist FFPE", "role": "candidate resource", "image_status": "20x Olympus VS200 H&E source-described; HEST dimensions 35637x29395; image/transform not independently checked", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "specimen": "human lung squamous cell carcinoma", "slide": "V42A20-354 D1", "reused_in": [ "HEST TENX62" ], "route_review": { "date": "2026-10-15", "status": "Vendor page requires registration and terms before download", "states": [ "vendor-terms", "local-qc" ], "next_step": "Complete the vendor registration if wanted (not done), then check the files, H&E and donor history.", "sections_with_matching_coordinates": null } } }, { "id": "pcpg-ling-ssrn", "label": "Ling et al., SSRN manuscript", "title": "Ling et al. integrated single-cell and spatial PCC profiling", "citation": { "authors": null, "title": "Ling et al. integrated single-cell and spatial PCC profiling", "journal": "SSRN", "year": null, "doi": null, "url": "https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5035122" }, "cancers": [ "PCPG" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Spatial transcriptomics (platform unverified)" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "release-unresolved", "package-unverified" ], "accession": null, "access": { "category": "unresolved", "route": "Author manuscript on SSRN; full-text retrieval blocked by a security check; no data release found", "links": [ [ "SSRN manuscript", "https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5035122" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Author manuscript on SSRN describing integrated single-cell and spatial profiling of pheochromocytoma. The spatial platform, sample count and data release were not verified, and an SSRN 'review complete' label does not establish peer review or release.", "compartments": [ "tumour-unspecified" ], "reported": [], "notes": [ "Verify final publication and data accession", "Do not infer release or peer review from SSRN review-complete label" ], "spatial_review": { "id": "pcpg-ling-ssrn", "date": "2026-10-15", "analysis_cohort": "PCPG", "assay_classes": [ "unverified" ], "platform": "spatial transcriptomics, platform/package unverified", "role": "unverified access lead", "image_status": "Histology described, original image package not found", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "route_review": { "date": "2026-10-15", "status": "Manuscript lead; data release unresolved", "states": [ "author-release" ], "next_step": "Ask the authors for the final publication, platform, patient and section counts, accession and expression and H&E package.", "sections_with_matching_coordinates": null } } }, { "id": "pcpg-developmental-preprint", "label": "Zhu et al. 2026, preprint", "title": "Spatially organized developmental cell states link paraganglioma and neuroblastoma through chromaffin-neuroblast plasticity", "citation": { "authors": "Zhu J, et al.", "title": "Spatially organized developmental cell states link paraganglioma and neuroblastoma through chromaffin-neuroblast plasticity", "journal": "bioRxiv (preprint)", "year": 2026, "doi": "10.64898/2026.04.07.715303", "url": "https://doi.org/10.64898/2026.04.07.715303" }, "cancers": [ "PCPG" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Spatial transcriptomics (human assay details unverified)" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "release-unresolved", "package-unverified" ], "accession": null, "access": { "category": "unreleased", "route": "No actionable accession; release promised at publication; human data described as controlled", "links": [ [ "Publication", "https://doi.org/10.64898/2026.04.07.715303" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Preprint on spatially organised developmental cell states linking paraganglioma and neuroblastoma. Its full text describes two human PPGL specimens (PPGL #1 and malignant PPGL #263) profiled with Visium HD; mouse in-situ sequencing, neuroblastoma and composite tumours are separate analyses. An adjacent H&E inset is shown for PPGL #1, but original same-section images are not established. The data statement promises public accessions but supplies none, and describes de-identified human data as controlled under ethics approval and data agreements.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 2, "human PPGL specimens", "preprint full text" ] ], "notes": [ "Separate human PCC/PGL from mouse, neuroblastoma and composite tumours", "A virtual TCGA spatial atlas is predicted expression and cannot fill this gap", "An earlier version of the preprint was titled 'Sympathoadrenal lineage plasticity following KIF1Bβ-NF1 loss'.", "Count only the two human PPGL specimens; exclude mouse, neuroblastoma and composite tumours" ], "spatial_review": { "id": "pcpg-developmental-preprint", "date": "2026-10-15", "analysis_cohort": "PCPG", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium HD (two human PPGL specimens)", "role": "unverified access lead", "image_status": "Adjacent H&E inset shown for PPGL #1; original images not released", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "title_alias": "Sympathoadrenal lineage plasticity following KIF1Bβ-NF1 loss; preprint title changed", "route_review": { "date": "2026-10-15", "status": "Human Visium HD assay resolved; accession not supplied", "states": [ "author-release" ], "next_step": "Ask the lead contact for the accession and the human PPGL processed data, coordinates, original H&E, section relation and donor and treatment metadata.", "sections_with_matching_coordinates": null } } }, { "id": "prad-10x-acinar", "label": "10x Genomics prostate acinar carcinoma, Visium FFPE", "title": "Human prostate cancer, acinar cell carcinoma (FFPE)", "citation": { "authors": "10x Genomics", "title": "Human prostate cancer, acinar cell carcinoma (FFPE)", "journal": "10x Genomics datasets", "year": null, "doi": null, "url": "https://www.10xgenomics.com/datasets/human-prostate-cancer-acinar-cell-carcinoma-ffpe-1-standard" }, "cancers": [ "PRAD" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "listed-together", "gates": [ "he-unverified", "identity", "treatment-review" ], "accession": "10x Genomics dataset; block 1D1061-Tp11", "access": { "category": "account", "route": "Vendor dataset page; downloading requires registration and acceptance of the vendor's terms (CC BY 4.0 data). No registration was made.", "links": [ [ "Vendor dataset", "https://www.10xgenomics.com/datasets/human-prostate-cancer-acinar-cell-carcinoma-ffpe-1-standard" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Vendor Visium FFPE demonstration of one prostate acinar adenocarcinoma specimen (block 1D1061-Tp11), with Gleason score 7 and stage IV as reported by the vendor. A 20x Metafer H&E is source-described; the full image and registration were not checked, and prior hormonal or systemic therapy is unknown.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 1, "sample (vendor specimen)", "vendor dataset page" ] ], "notes": [ "Retain Gleason score 7 and reported stage as vendor annotations", "Do not assume distinct independent patients across vendor pages", "Review prior ADT/systemic therapy and tissue compartment", "Vendor download requires registration and acceptance of terms; no form was submitted" ], "spatial_review": { "id": "prad-10x-acinar", "date": "2026-10-15", "analysis_cohort": "PRAD", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium FFPE", "role": "candidate resource", "image_status": "20x Metafer H&E source-described; full image and registration check pending", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "block": "1D1061-Tp11", "reported_stage": "IV", "reported_gleason": 7, "route_review": { "date": "2026-10-15", "status": "Vendor page requires registration and terms before download", "states": [ "vendor-terms", "local-qc" ], "next_step": "Complete the vendor registration if wanted (not done), then check the files, H&E and donor history.", "sections_with_matching_coordinates": null } } }, { "id": "prad-10x-invasive", "label": "10x Genomics prostate invasive adenocarcinoma, Visium FFPE", "title": "Human prostate cancer, adenocarcinoma with invasive carcinoma (FFPE)", "citation": { "authors": "10x Genomics", "title": "Human prostate cancer, adenocarcinoma with invasive carcinoma (FFPE)", "journal": "10x Genomics datasets", "year": null, "doi": null, "url": "https://www.10xgenomics.com/datasets/human-prostate-cancer-adenocarcinoma-with-invasive-carcinoma-ffpe-1-standard-1-3-0" }, "cancers": [ "PRAD" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "listed-together", "gates": [ "he-unverified", "identity", "treatment-review" ], "accession": "10x Genomics dataset; block 1E500_Tp12", "access": { "category": "account", "route": "Vendor dataset page; downloading requires registration and acceptance of the vendor's terms (CC BY 4.0 data). No registration was made.", "links": [ [ "Vendor dataset", "https://www.10xgenomics.com/datasets/human-prostate-cancer-adenocarcinoma-with-invasive-carcinoma-ffpe-1-standard-1-3-0" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Vendor Visium FFPE demonstration of one prostate adenocarcinoma with invasive carcinoma (block 1E500_Tp12), with Gleason score 7 and stage III as reported by the vendor. The two vendor prostate pages are not assumed to come from distinct patients. A 20x Metafer H&E is source-described; the full image, registration and treatment history were not checked.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 1, "sample (vendor specimen)", "vendor dataset page" ] ], "notes": [ "Retain Gleason score 7 and reported stage as vendor annotations", "Do not assume distinct independent patients across vendor pages", "Review prior ADT/systemic therapy and tissue compartment", "Vendor download requires registration and acceptance of terms; no form was submitted" ], "spatial_review": { "id": "prad-10x-invasive", "date": "2026-10-15", "analysis_cohort": "PRAD", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium FFPE", "role": "candidate resource", "image_status": "20x Metafer H&E source-described; full image and registration check pending", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "block": "1E500_Tp12", "reported_stage": "III", "reported_gleason": 7, "route_review": { "date": "2026-10-15", "status": "Vendor page requires registration and terms before download", "states": [ "vendor-terms", "local-qc" ], "next_step": "Complete the vendor registration if wanted (not done), then check the files, H&E and donor history.", "sections_with_matching_coordinates": null } } }, { "id": "prad-hirz-slideseq", "label": "Hirz et al. 2023", "title": "Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses", "citation": { "authors": "Hirz T, et al.", "title": "Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses", "journal": "Nature Communications", "year": 2023, "doi": "10.1038/s41467-023-36325-2", "url": "https://doi.org/10.1038/s41467-023-36325-2" }, "cancers": [ "PRAD" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Slide-seqV2" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "serial-section", "gates": [ "coordinates", "serial-section", "he-not-located", "identity" ], "accession": "Zenodo 7526696", "access": { "category": "open", "route": "public Zenodo archive; GEO GSE181294 is primarily scRNA; use spatial archive", "links": [ [ "Publication", "https://doi.org/10.1038/s41467-023-36325-2" ], [ "Full text (PMC)", "https://pmc.ncbi.nlm.nih.gov/articles/PMC9905093/" ], [ "Spatial archive", "https://zenodo.org/records/7526696" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Slide-seqV2 profiling within a study of the prostate tumour microenvironment: 12 arrays from four donors, two with prostate cancer from a treatment-naive prostatectomy cohort and two controls without prostate cancer. H&E comes from consecutive sections, not the assayed ones. The study's 19 cancer patients are single-cell RNA-seq donors, not spatial patients. The public Zenodo archive has count matrices and annotations for the 12 arrays, but all 12 bead-location tables are defective (missing bead barcodes and x and y values) and the archive contains no H&E; archived code refers to local coordinate files that were not released. The data are not spatially usable until corrected coordinates are released.", "compartments": [ "primary-tumour", "normal" ], "reported": [ [ 2, "prostate cancer donors", "publication" ], [ 2, "control donors without prostate cancer", "publication" ], [ 4, "spatial donors in all", "publication" ], [ 12, "Slide-seqV2 arrays", "publication" ] ], "notes": [ "Do not transpose 19 scRNA cancer patients into spatial patient counts", "Keep bladder-cancer prostate controls separate from cancer patients", "Map 12 arrays/replicates to tissue, donor and H&E", "All 12 released bead-location tables are defective; do not treat the package as spatially usable" ], "spatial_review": { "id": "prad-hirz-slideseq", "date": "2026-10-15", "analysis_cohort": "PRAD", "assay_classes": [ "whole-transcriptome" ], "platform": "Slide-seqV2", "role": "candidate resource", "image_status": "No H&E in the public archive; consecutive-section H&E not released", "treatment_status": "two tumour donors from treatment-naive prostatectomy cohort", "treatment_class": "reported-untreated", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "route_review": { "date": "2026-10-15", "status": "Bead coordinates defective in all 12 released tables", "states": [ "author-release" ], "next_step": "Ask the study authors for corrected bead locations or the per-array input files, the barcode crosswalk and original serial H&E.", "sections_with_matching_coordinates": null } } }, { "id": "prad-erickson-clonal", "label": "Erickson et al. 2022", "title": "Spatially resolved clonal copy number alterations in benign and malignant tissue", "citation": { "authors": "Erickson A, et al.", "title": "Spatially resolved clonal copy number alterations in benign and malignant tissue", "journal": "Nature", "year": 2022, "doi": "10.1038/s41586-022-05023-2", "url": "https://doi.org/10.1038/s41586-022-05023-2" }, "cancers": [ "PRAD" ], "layer": "matched-spatial", "status": "candidate", "modalities": [ "spatial-rna" ], "techniques": [ "Spatial Transcriptomics (legacy arrays)", "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "platform", "package-unverified", "identity" ], "accession": "Mendeley Data svw96g68dv (version 5)", "access": { "category": "open", "route": "Public Mendeley release (versions 1 and 5); file downloads failed technically; raw sequencing controlled at EGA", "links": [ [ "Publication", "https://doi.org/10.1038/s41586-022-05023-2" ], [ "Data archive", "https://data.mendeley.com/datasets/svw96g68dv/5" ], [ "Data archive, version 1", "https://data.mendeley.com/datasets/svw96g68dv/1" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Legacy Spatial Transcriptomics and Visium study mapping clonal copy-number alterations across benign and malignant prostate tissue. The public Mendeley release lists original-image folders for two patients (Patient 1, with legacy-array and Visium folders, and Patient 2), with large JPEG files and a checksum, but the actual file downloads failed (an HTTP error and a browser timeout): a technical gap, not a permission requirement. Benign fields and multiple regions from one patient must not be counted as separate patients. Controlled raw sequencing at EGA is not needed for processed reuse.", "compartments": [ "tumour-unspecified", "normal" ], "reported": [ [ 2, "patients with public image folders", "Mendeley release" ] ], "notes": [ "Keep benign fields separate; do not count multiple axial regions as patients", "Public image folders verified for two patients; actual files still to retrieve" ], "spatial_review": { "id": "prad-erickson-clonal", "date": "2026-10-15", "analysis_cohort": "PRAD", "assay_classes": [ "whole-transcriptome" ], "platform": "legacy Spatial Transcriptomics", "role": "additional public candidate", "image_status": "Original-image folders and large JPEGs listed publicly; downloads failed", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "route_review": { "date": "2026-10-15", "status": "Public image folders verified; file download failed", "states": [ "download-failure", "local-qc" ], "next_step": "Retry the public file downloads, then check images, coordinates and the clinical mapping.", "sections_with_matching_coordinates": null } } }, { "id": "stad-gse251950", "label": "Lee et al. 2024", "title": "Spatial dissection of tumour microenvironments in gastric cancers reveals the immunosuppressive crosstalk between CCL2+ fibroblasts and STAT3-activated macrophages", "citation": { "authors": "Lee SH, et al.", "title": "Spatial dissection of tumour microenvironments in gastric cancers reveals the immunosuppressive crosstalk between CCL2+ fibroblasts and STAT3-activated macrophages", "journal": "Gut", "year": 2024, "doi": "10.1136/gutjnl-2024-332901", "url": "https://doi.org/10.1136/gutjnl-2024-332901" }, "cancers": [ "STAD" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "listed-together", "gates": [ "identity", "treatment-review", "he-not-located", "image-qc", "calibration" ], "accession": "GSE251950", "access": { "category": "open", "route": "public processed GEO; raw SRA", "links": [ [ "GEO series", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE251950" ], [ "Publication", "https://doi.org/10.1136/gutjnl-2024-332901" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Visium sections from nine gastric cancer donor labels: nine primary tumours and one metastasis (GC6-PM, from the same donor as GC6), kept separate. Space Ranger archives include H&E previews; the original scans were not verified.", "compartments": [ "primary-tumour", "metastatic-tumour" ], "reported": [ [ 9, "donor labels", "GEO series" ], [ 9, "primary-tumour sections", "GEO series" ], [ 1, "metastasis section (GC6-PM, same donor as GC6)", "GEO series" ], [ 10, "spatial samples in all", "GEO series" ] ], "notes": [ "GC6 and GC6-PM are the same donor; keep GC6-PM metastatic", "Preserve histology and treatment metadata; original H&E/registration required", "Matched data with preview image: 10 checked section packages, not yet listed as individual section records" ], "spatial_review": { "id": "stad-gse251950", "date": "2026-10-15", "analysis_cohort": "STAD", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium", "role": "candidate resource", "image_status": "All ten section packages checked: exact barcode-coordinate agreement; images 2,000-pixel outputs only; original scans not found", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": { "metastatic_sample_ids": [ "GSM7990479" ] }, "route_review": { "date": "2026-10-15", "status": "Ten section packages checked; preview images only", "states": [ "public-download", "author-release", "local-qc" ], "next_step": "Ask the submitter for original scans and the clinical, histology and treatment linkage for the nine donor labels and the GC6 peritoneal metastasis.", "sections_with_matching_coordinates": 10 } }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "stad-gse270678", "label": "Gao et al. 2026", "title": "A spatially resolved atlas of gastric cancer characterises a lymphocyte-aggregated region", "citation": { "authors": "Gao S, et al.", "title": "A spatially resolved atlas of gastric cancer characterises a lymphocyte-aggregated region", "journal": "Nature Communications", "year": 2026, "doi": "10.1038/s41467-026-68612-z", "url": "https://doi.org/10.1038/s41467-026-68612-z" }, "cancers": [ "STAD" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "listed-together", "gates": [ "he-not-located", "image-qc", "calibration" ], "accession": "GSE270678; HRA007814 (raw, controlled)", "access": { "category": "open", "route": "public processed GEO; raw HRA007814 controlled", "links": [ [ "GEO series", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE270678" ], [ "Publication", "https://doi.org/10.1038/s41467-026-68612-z" ], [ "Additional Mendeley release", "https://data.mendeley.com/datasets/559mchb37p/1" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Visium atlas of lymphocyte-aggregated regions in gastric cancer: 33 main sections from 19 patients and 39 repeat sections; donor D30 appears only among the repeats, which gives 20 donor labels in the deposit. All 72 deposited section packages have expression barcodes that match their tissue coordinates exactly; the images are 2,000-pixel previews. The paper reports treatment-naive surgical donors; histology (intestinal, diffuse, indeterminate) and core, edge and in-between regions are annotated. An additional Mendeley release holds one 6.12 GB spatial RDS file, whose download failed (a technical gap). Raw reads (HRA007814) are controlled and are not needed for processed reuse.", "compartments": [ "primary-tumour" ], "reported": [ [ 19, "patients with main sections", "Supplementary Data 1" ], [ 33, "main sections", "Supplementary Data 1" ], [ 39, "repeat sections", "Supplementary Data 1" ], [ 20, "donor labels in the deposit, D30 in repeats only", "GEO series" ], [ 72, "deposited sections", "GEO series" ] ], "notes": [ "Do not count 72 sections as patients", "Preserve intestinal/diffuse/indeterminate histology and core/edge/in-between compartments", "Recover original-resolution H&E", "Repeat sections add sections, not patients; D30 appears only among the repeats", "Matched data with preview image: 72 checked section packages, not yet listed as individual section records" ], "spatial_review": { "id": "stad-gse270678", "date": "2026-10-15", "analysis_cohort": "STAD", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium", "role": "candidate resource", "image_status": "All 72 section packages checked: exact barcode-coordinate agreement; 2,000-pixel previews; original scans not found", "treatment_status": "paper reports treatment-naive surgical donors", "treatment_class": "reported-untreated", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": {}, "route_review": { "date": "2026-10-15", "status": "72 section packages checked; patient and section count resolved", "states": [ "public-download", "download-failure", "author-release", "local-qc" ], "next_step": "Retry the Mendeley download; ask the submitter for original scans and calibration if they are not in the public RDS.", "sections_with_matching_coordinates": 72 } }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "ucec-barkley-gse203612", "label": "Barkley et al. 2022, UCEC sample", "title": "Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment", "citation": { "authors": "Barkley D, et al.", "title": "Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment", "journal": "Nature Genetics", "year": 2022, "doi": "10.1038/s41588-022-01141-9", "url": "https://doi.org/10.1038/s41588-022-01141-9" }, "cancers": [ "UCEC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium" ], "preservation": [], "specimen": "clinical-tumour", "linkage": "listed-together", "gates": [ "treatment-review", "pathology-review", "he-not-located", "image-qc", "calibration" ], "accession": "GSE203612 (UCEC spatial sample GSM6177623)", "access": { "category": "open", "route": "public processed GEO", "links": [ [ "GEO series", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203612" ], [ "Publication", "https://doi.org/10.1038/s41588-022-01141-9" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "One endometrial carcinoma Visium sample (GSM6177623, NYU_UCEC3_Vis) from a pan-cancer cell-state atlas; single-cell samples and other cancers in the series are not part of this entry. Its section package was checked (expression barcodes match the tissue coordinates), but the deposited image is a 1,899 × 2,000-pixel preview. The author-linked Dropbox and NYU SharePoint data folders are deleted or disabled, and the archived code on Zenodo (6611786) contains scripts only, without the original scan or clinical table. Histological subtype and treatment history are unknown.", "compartments": [ "tumour-unspecified" ], "reported": [ [ 1, "endometrial carcinoma spatial sample (GSM6177623)", "GEO series" ] ], "notes": [ "Use only GSM6177623/NYU_UCEC3_Vis for UCEC spatial entry", "Do not count scRNA samples or other cancers as UCEC spatial", "Recover original scan, subtype, treatment and registration", "Author-linked data folders are disabled; the archived code contains no original scan or clinical table", "Matched data with preview image: 1 checked section packages, not yet listed as individual section records" ], "spatial_review": { "id": "ucec-barkley-gse203612", "date": "2026-10-15", "analysis_cohort": "UCEC", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium", "role": "candidate resource", "image_status": "GSM6177623 section package checked; image is a 1,899 × 2,000-pixel preview; author data links disabled", "treatment_status": "unknown", "treatment_class": "unknown", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": { "sample_ids": [ "GSM6177623" ] }, "route_review": { "date": "2026-10-15", "status": "Section package checked; author data links disabled", "states": [ "public-download", "author-release", "local-qc" ], "next_step": "Ask the study team to restore the public data links and for the original image, histological subtype and treatment of NYU_UCEC3.", "sections_with_matching_coordinates": 1 } }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "ucec-np137-gse225690", "label": "Cassier et al. 2023, NP137 trial", "title": "Netrin-1 blockade inhibits tumour growth and EMT features in endometrial cancer", "citation": { "authors": "Cassier PA, et al.", "title": "Netrin-1 blockade inhibits tumour growth and EMT features in endometrial cancer", "journal": "Nature", "year": 2023, "doi": "10.1038/s41586-023-06367-z", "url": "https://doi.org/10.1038/s41586-023-06367-z" }, "cancers": [ "UCEC" ], "layer": "matched-spatial", "status": "preview", "modalities": [ "spatial-rna" ], "techniques": [ "Visium FFPE" ], "preservation": [ "FFPE" ], "specimen": "clinical-tumour", "linkage": "unverified", "gates": [ "treated", "he-not-located", "image-qc", "calibration" ], "accession": "GSE225690", "access": { "category": "open", "route": "public processed GEO", "links": [ [ "GEO series", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE225690" ], [ "Publication", "https://doi.org/10.1038/s41586-023-06367-z" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Visium FFPE profiles of endometrial cancer metastasis biopsies from the NP137 netrin-1 blockade trial: four sections from two patients, each at baseline and after one month of NP137. The trial supplement identifies 01-034 as endometrioid adenocarcinoma (initial grade 2) and 01-039 as papillary serous adenocarcinoma (initial grade 3), and every trial participant had received at least two earlier lines of systemic therapy (two to six, median three), so both patients were previously treated even at baseline. All four section packages have expression barcodes that match their tissue coordinates exactly (539 to 2,141 spots); the images are previews of at most 2,000 pixels. An exploratory treated, metastatic comparison of two histologies, not a homogeneous endometrioid reference.", "compartments": [ "metastatic-tumour" ], "reported": [ [ 2, "patients", "trial publication" ], [ 4, "metastasis biopsy sections profiled", "GEO series" ], [ 2, "timepoints per patient (baseline and after one month)", "GEO series" ] ], "notes": [ "All four samples are metastatic biopsies", "Use for exploratory treatment effects, not untreated primary reference", "Two histologies: 01-034 endometrioid (initial grade 2) and 01-039 papillary serous (initial grade 3); do not pool as one endometrioid reference", "Both patients had at least two earlier systemic lines; baseline means before NP137", "Matched data with preview image: 4 checked section packages, not yet listed as individual section records" ], "spatial_review": { "id": "ucec-np137-gse225690", "date": "2026-10-15", "analysis_cohort": "UCEC", "assay_classes": [ "whole-transcriptome" ], "platform": "Visium FFPE", "role": "exploratory treated/metastatic spatial comparison", "image_status": "All four section packages checked: exact barcode-coordinate agreement; previews of at most 2,000 pixels", "treatment_status": "every trial participant had two to six earlier systemic lines; sampled at baseline and after one month of NP137", "treatment_class": "baseline-and-on-treatment", "eligible_patients": null, "strict_core_promoted": false, "sample_ids": { "sample_ids": [ "GSM7054270", "GSM7054271", "GSM7054272", "GSM7054273" ] }, "route_review": { "date": "2026-10-15", "status": "Two previously treated patients and four sections confirmed", "states": [ "public-download", "author-release", "local-qc" ], "next_step": "Ask the trial team for original H&E and calibration, and for exact earlier regimens only if a response analysis needs them.", "sections_with_matching_coordinates": 4 } }, "followup_review": { "date": "2026-10-16", "checks": [ { "check": "Original scans", "depth": "public series/supplementary listings and source data routes; earlier complete package checks reused; primary availability re-read where retrieved", "result": "No further original scan matched to the expression and coordinates in the public listings and data routes checked." } ] } }, { "id": "tcga-cesc", "label": "TCGA-CESC", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-CESC" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "CESC" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "CESC", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-CESC" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Cervical squamous cell carcinoma and endocervical adenocarcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. The selected cohort is cervical squamous cell carcinoma (CSCC), using histology from the TCGA cervical study with the GDC label as fallback. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked.", "notes": [ "Analysed as cervical squamous cell carcinoma (CSCC, 249 patients, 248 with both assays). The 46 adenocarcinomas and six adenosquamous carcinomas are outside the selected cohort; their assays are not marked as failed.", "Publication and GDC histology differ for three cases; both labels are kept.", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "CSCC" }, { "id": "tcga-esca", "label": "TCGA-ESCA", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-ESCA" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "ESCA" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "ESCA", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-ESCA" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Oesophageal carcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked beyond the histology review.", "notes": [ "The project combines squamous cell carcinoma and adenocarcinoma. A histology-defined cohort of 90 confirmed ESCC patients, all with RNA-seq and 450k, is used for analysis as an approved exception to the general screen; see the oesophageal carcinoma page.", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "ESCC" }, { "id": "tcga-kirc", "label": "TCGA-KIRC", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-KIRC" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "KIRC" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "KIRC", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-KIRC" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Kidney renal clear cell carcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Separate project from papillary renal cell carcinoma (KIRP).", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "KIRC" }, { "id": "tcga-kirp", "label": "TCGA-KIRP", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-KIRP" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "KIRP" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "KIRP", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-KIRP" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Kidney renal papillary cell carcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Separate project from clear cell renal cell carcinoma (KIRC).", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "KIRP" }, { "id": "tcga-lusc", "label": "TCGA-LUSC", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-LUSC" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "LUSC" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "LUSC", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-LUSC" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Lung squamous cell carcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "LUSC" }, { "id": "tcga-pcpg", "label": "TCGA-PCPG", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-PCPG" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "PCPG" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "PCPG", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-PCPG" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Pheochromocytoma and paraganglioma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Analysed as one pooled cohort with location, publication-first histology, molecular subtype and adrenal-cortical admixture annotations. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked.", "notes": [ "Pooled PCPG (178 patients, all with both assays): 146 pheochromocytomas and 32 paragangliomas. Two pathology-confirmed head and neck paragangliomas are retained; a sensitivity subset without them has 176 patients.", "Historical benign and malignant codes do not determine eligibility.", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "PCPG" }, { "id": "tcga-prad", "label": "TCGA-PRAD", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-PRAD" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "PRAD" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "PRAD", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-PRAD" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Prostate adenocarcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Many tumour aliquots were excluded by the pathology group for RNA degradation.", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "PRAD" }, { "id": "tcga-stad", "label": "TCGA-STAD", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-STAD" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "STAD" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "STAD", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "histology-strata", "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-STAD" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Stomach adenocarcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked; histology strata have not yet been curated.", "notes": [ "Gastro-oesophageal junction tumours need site review against ESCA.", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "STAD" }, { "id": "tcga-ucec", "label": "TCGA-UCEC", "citation": { "authors": "The Cancer Genome Atlas Research Network", "title": null, "journal": "NCI Genomic Data Commons", "year": null, "doi": null, "url": "https://portal.gdc.cancer.gov/projects/TCGA-UCEC" }, "related_citations": [ { "authors": "Liu J, et al.", "title": "An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics", "journal": "Cell", "year": 2018, "doi": "10.1016/j.cell.2018.02.052", "url": "https://doi.org/10.1016/j.cell.2018.02.052" } ], "cancers": [ "UCEC" ], "layer": "wsi-bulk", "status": "screened", "tcga_project": "UCEC", "modalities": [ "he-wsi", "bulk-rna", "methylation-450k", "raw-reads", "normal-reference" ], "techniques": [ "Diagnostic and tissue slides", "RNA-seq", "Illumina 450k methylation" ], "preservation": [ "FFPE", "Fresh frozen" ], "specimen": "clinical-tumour", "compartments": [ "primary-tumour", "solid-normal" ], "linkage": "same-patient", "gates": [ "tumour-slide-linkage", "image-qc" ], "access": { "category": "open", "route": "Slide images, processed RNA-seq, methylation beta values and clinical data are open on the GDC; raw sequencing reads are controlled through dbGaP. PanCanAtlas harmonized matrices and quality annotations are open downloads.", "links": [ [ "GDC project", "https://portal.gdc.cancer.gov/projects/TCGA-UCEC" ], [ "PanCanAtlas data", "https://gdc.cancer.gov/about-data/publications/pancanatlas" ] ] }, "verification": "metadata-checked", "verified_on": "2026-10-15", "description": "Uterine corpus endometrial carcinoma. Slide images, RNA-seq and Illumina 450k methylation from the same patients, with solid normal tissue from some patients. Analysed as one pooled cohort with publication-first histology, grade and molecular-group annotations. Counts are shown after PanCanAtlas assay exclusions, after a patient-level treatment and diagnosis screen, and for the selected analysis set. Tumour slide linkage and image QC have not yet been checked.", "notes": [ "Pooled endometrial carcinoma (523 patients, 413 with both assays) with an endometrioid-only sensitivity subset (398 / 303). Nineteen publication and GDC histology labels differ; both are kept. Uterine carcinosarcoma is not added.", "Normal tissue comes from patients with cancer, usually adjacent to the tumour. It is not a healthy-donor control." ], "analysis_cohort": "UCEC" } ]