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Tabula Sapiens (483k) (Kedzierska et al. 2025)

Tabula Sapiens (Figshare TabulaSapiens.h5ad.zip): cells from 24 tissues across 15 donors; 483k cells, 177 labels, 27 batches.

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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 Tabula Sapiens (483k) 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 Tabula Sapiens (483k) 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 Tabula Sapiens (Figshare TabulaSapiens.h5ad.zip): cells from 24 tissues across 15 donors; 483k cells, 177 labels, 27 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 Tabula Sapiens (Figshare TabulaSapiens.h5ad.zip): cells from 24 tissues across 15 donors; 483k cells, 177 labels, 27 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-tabula-sapiens-483k

areas: single-cell
contexts: research
source dataset label: Tabula Sapiens (483k)
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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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: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.14 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 Tabula Sapiens (483k) (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 Q20, metric block 'ARI', row 'Tabula Sapiens (483k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.41 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 Tabula Sapiens (483k) (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 Q8, metric block 'ASW', row 'Tabula Sapiens (483k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.45 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 Tabula Sapiens (483k) (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 Q41, metric block 'Average batch', row 'Tabula Sapiens (483k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.3 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 Tabula Sapiens (483k) (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 Q26, metric block 'AvgBIO', row 'Tabula Sapiens (483k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.9 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 Tabula Sapiens (483k) (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 Q31, metric block 'Batch integration', row 'Tabula Sapiens (483k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.35 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 Tabula Sapiens (483k) (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 Q14, metric block 'NMI', row 'Tabula Sapiens (483k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (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 Tabula Sapiens (483k) (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 Q36, metric block 'PCR', row 'Tabula Sapiens (483k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (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 Tabula Sapiens (483k) (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 G10, row 'Geneformer', column 'Tabula Sapiens (483k)'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.27 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 Tabula Sapiens (483k) (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 E20, metric block 'ARI', row 'Tabula Sapiens (483k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.39 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 Tabula Sapiens (483k) (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 E8, metric block 'ASW', row 'Tabula Sapiens (483k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.41 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 Tabula Sapiens (483k) (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 E41, metric block 'Average batch', row 'Tabula Sapiens (483k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.39 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 Tabula Sapiens (483k) (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 E26, metric block 'AvgBIO', row 'Tabula Sapiens (483k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.74 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 Tabula Sapiens (483k) (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 E31, metric block 'Batch integration', row 'Tabula Sapiens (483k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.51 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 Tabula Sapiens (483k) (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 E14, metric block 'NMI', row 'Tabula Sapiens (483k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.08 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 Tabula Sapiens (483k) (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 E36, metric block 'PCR', row 'Tabula Sapiens (483k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	7 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 Tabula Sapiens (483k) (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 G4, row 'Harmony', column 'Tabula Sapiens (483k)'
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.28 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 Tabula Sapiens (483k) (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 C20, metric block 'ARI', row 'Tabula Sapiens (483k)', 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: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.48 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 Tabula Sapiens (483k) (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 C8, metric block 'ASW', row 'Tabula Sapiens (483k)', 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: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.47 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 Tabula Sapiens (483k) (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 C41, metric block 'Average batch', row 'Tabula Sapiens (483k)', 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: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.45 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 Tabula Sapiens (483k) (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 C26, metric block 'AvgBIO', row 'Tabula Sapiens (483k)', 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: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.93 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 Tabula Sapiens (483k) (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 C31, metric block 'Batch integration', row 'Tabula Sapiens (483k)', 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: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.58 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 Tabula Sapiens (483k) (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 C14, metric block 'NMI', row 'Tabula Sapiens (483k)', 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: Tabula Sapiens (483k) (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 HVG cell embedding on Tabula Sapiens (483k) (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 C36, metric block 'PCR', row 'Tabula Sapiens (483k)', 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: Tabula Sapiens (483k) (Kedzierska et al. 2025)	3 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 Tabula Sapiens (483k) (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 G5, row 'HVG', column 'Tabula Sapiens (483k)'
Configuration: scGPT blood (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.31 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 Tabula Sapiens (483k) (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 M20, metric block 'ARI', row 'Tabula Sapiens (483k)', column 'scGPT blood' (single-value column)