Human Gut Cell Atlas (HGCA) v1.0
Source datasets are AnnData (.h5ad) files that conform to the HCA metadata schema and were used to construct the atlas's integrated objects.
| File Name / Study | Assay | Tissue | Disease | Cell Count | Primary Data (fastqs) | Download |
|---|---|---|---|---|---|---|
hgca-v1-arends-helmsley-r1.h5ad Mark Arends, M.Arends@ed.ac.uk - Unpublished | 10x 3' v2 | ileum | normal | 18,690 | ||
hgca-v1-basu-helmsley-r1.h5ad Basu - Unpublished | 10x 3' v3 | 2 tissues | normal | 103,385 | ||
hgca-v1-burclaff-2022-r1.h5ad | 10x 3' v3 | 6 tissues | normal | 10,389 | HCA Explorer (opens in a new tab) | |
hgca-v1-dominguez-2022-r1.h5ad | 10x 5' v1 | 3 tissues | normal | 1,494 | HCA Explorer (opens in a new tab) | |
hgca-v1-egozi-2023-r1.h5ad | 10x 3' v3 | ileum | 2 diseases | 106 | HCA Explorer (opens in a new tab) | |
hgca-v1-elmentaite-2020-r1.h5ad | 10x 3' v2 | 11 tissues | normal | 59,884 | ||
hgca-v1-hamilton-helmsley-r1.h5ad | 10x 3' v3 | ascending colon | normal | 48,760 | ||
hgca-v1-he-2020-r1.h5ad | 10x 5' v1 | 3 tissues | normal | 12,315 | ||
hgca-v1-huang-2019-r1.h5ad | 10x 5' v3 | colon | normal | 20,869 | ||
hgca-v1-jaeger-2021-r1.h5ad | 10x 3' v2 | ileum | 2 diseases | 19,072 | ||
hgca-v1-james-2020-3p-r1.h5ad | 10x 3' v2 | 4 tissues | normal | 28,571 | ||
hgca-v1-james-2020-5p-r1.h5ad | 10x 5' v2 | 4 tissues | normal | 4,599 | ||
hgca-v1-kinchen-2018-r1.h5ad | 10x 3' v2 | colon | normal | 8,187 | ||
hgca-v1-kong-2023-v2-r1.h5ad | 10x 3' v2 | ileum | normal Crohn disease | 17,037 | HCA Explorer (opens in a new tab) | |
hgca-v1-kong-2023-v3-r1.h5ad | 10x 3' v3 | ileum | normal Crohn disease | 108,360 | HCA Explorer (opens in a new tab) | |
hgca-v1-krzak-2023-r1.h5ad | 10x 3' v3 | 2 tissues | normal | 111,869 | ||
hgca-v1-lee-2020-r1.h5ad | 10x 3' v2 | 5 tissues | colorectal cancer | 14,483 | ||
hgca-v1-luoma-2020-r1.h5ad | 10x 5' v1 | colon | normal enteritis | 78,364 | HCA Explorer (opens in a new tab) | |
hgca-v1-maddipatla-2023-r1.h5ad | 10x 5' v1 | ileum | normal | 3,496 | HCA Explorer (opens in a new tab) | |
hgca-v1-martin-2019-r1.h5ad | 10x 3' v2 | ileum | Crohn disease | 19,903 | ||
hgca-v1-parikh-2019-r1.h5ad | 10x 3' v2 | colon | normal | 4,424 | ||
hgca-v1-uzzan-2022-r1.h5ad | 10x 3' v2 | colon | normal | 16,491 | ||
hgca-v1-wang-2020-r1.h5ad | 10x 3' v2 | 3 tissues | 2 diseases | 15,283 | ||
hgca-v1-wells-2025-2-r1.h5ad | 10x 3' v3 | 2 tissues | normal | 154,106 | HCA Explorer (opens in a new tab) | |
hgca-v1-wells-2025-r1.h5ad | 10x 5' v2 | jejunum | normal | 38,042 | HCA Explorer (opens in a new tab) | |
hgca-v1-yu-2021-r1.h5ad | 10x 3' v2 | duodenum | normal | 8,619 | ||
hgca-v1-zheng-2024-r1.h5ad | 10x 3' v2 | ileum | digestive system disorder | 17,704 | HCA Explorer (opens in a new tab) |