Dataset subset

Immune (330k) (Kedzierska et al. 2025)

Cross-tissue Immune Cell Atlas: immune cells from 16 tissues across 12 adult donors; 330k cells, 45 labels, 12 batches.

Evaluation results

16 evaluations · 128 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.19 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q19, metric block 'ARI', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.45 Scib asw label (cell-type ASW; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q7, metric block 'ASW', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.38 Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q40, metric block 'Average batch', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.35 Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q25, metric block 'AvgBIO', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.76 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q30, metric block 'Batch integration', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.42 Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q13, metric block 'NMI', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0 Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q35, metric block 'PCR', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	8 Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell F10, row 'Geneformer', column 'Immune (330k)'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.51 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E19, metric block 'ARI', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.52 Scib asw label (cell-type ASW; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E7, metric block 'ASW', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.74 Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E40, metric block 'Average batch', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.57 Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E25, metric block 'AvgBIO', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.8 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E30, metric block 'Batch integration', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.67 Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E13, metric block 'NMI', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.67 Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E35, metric block 'PCR', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	1 Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell F4, row 'Harmony', column 'Immune (330k)'
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.41 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C19, metric block 'ARI', row 'Immune (330k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.51 Scib asw label (cell-type ASW; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C7, metric block 'ASW', row 'Immune (330k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.5 Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C40, metric block 'Average batch', row 'Immune (330k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.53 Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C25, metric block 'AvgBIO', row 'Immune (330k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.95 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C30, metric block 'Batch integration', row 'Immune (330k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.68 Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C13, metric block 'NMI', row 'Immune (330k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.05 Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C35, metric block 'PCR', row 'Immune (330k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	4 Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell F5, row 'HVG', column 'Immune (330k)'
Configuration: scGPT blood (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.4 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source scGPT blood cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell M19, metric block 'ARI', row 'Immune (330k)', column 'scGPT blood' (single-value column)

Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.

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Release 2026-10-23-5347695500ed · Evidence verified: Not verified

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14 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statement	Original source and location	Review and provenance
Source dataset label Immune (330k) Context-only references	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_dataset_label` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source dataset label Immune (330k) Context-only references	Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_dataset_label` Source artifact SHA-256: `8efcc5fcb2e35b9a04b1ee9e03581e20fffeb5521a4a4c748a6f9b34f7d3c47f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Context-only references	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Context-only references	Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `8efcc5fcb2e35b9a04b1ee9e03581e20fffeb5521a4a4c748a6f9b34f7d3c47f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split No split; each whole dataset is embedded and scored Context-only references	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split No split; each whole dataset is embedded and scored Context-only references	Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `8efcc5fcb2e35b9a04b1ee9e03581e20fffeb5521a4a4c748a6f9b34f7d3c47f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Cross-tissue Immune Cell Atlas: immune cells from 16 tissues across 12 adult donors; 330k cells, 45 labels, 12 batches. Context-only references	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Cross-tissue Immune Cell Atlas: immune cells from 16 tissues across 12 adult donors; 330k cells, 45 labels, 12 batches. Context-only references	Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `8efcc5fcb2e35b9a04b1ee9e03581e20fffeb5521a4a4c748a6f9b34f7d3c47f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: used in gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Context-only references	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	not individually reviewed No individual claim review recorded Audit details Field: `links:used_in:gfm-guides-20261014-kedzierska2025-protocol-cell-embedding` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: used in gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Context-only references	Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `links:used_in:gfm-guides-20261014-kedzierska2025-protocol-cell-embedding` Source artifact SHA-256: `8efcc5fcb2e35b9a04b1ee9e03581e20fffeb5521a4a4c748a6f9b34f7d3c47f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-10-23-5347695500ed · Record review: source checked

2 source records and release history

Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) · Original source · Version of record, Genome Biology 26:101, published 2025-04-18
Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Original source · Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record

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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-kedzierska2025-data-immune-330k

areas: single-cell
contexts: research
source dataset label: Immune (330k)
split: No split; each whole dataset is embedded and scored
source locator: Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability'
missing metadata: version: reason: unreported

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