HuBMAP-wide data products contain consolidated data for all datasets of a particular assay type and tissue, across all datasets, assay variants, and data providers. RNA-seq data products are added as both raw and processed versions: 'raw' features gene expression count matrices from the HuBMAP RNA-seq pipeline, and 'processed' versions are the results of secondary analysis (normalization, filtering, dimensionality reduction, clustering) applied to the raw matrix.

Tissue TypeCreation TimeAssay TypeNumber of DatasetsTotal Raw CellsNumber Raw Cell TypesTotal Processed CellsNumber Processed Cell TypesRaw Data Product DownloadProcessed Data Product DownloadShiny App(All Versions)
Bladder June 23, 2025, 7:09 p.m. rna-seq 14 170943 NA 160161 NA Raw H5AD Processed H5AD Shiny App All versions of Bladder
Fallopian Tube (Left) June 25, 2025, 6:10 p.m. multiome-rna-atac 4 32329 NA 17397 NA Raw h5mu Processed h5mu NA All versions of Fallopian Tube (Left)
Fallopian Tube (Left) June 23, 2025, 7:09 p.m. rna-seq 16 34935 NA 14233 NA Raw H5AD Processed H5AD Shiny App All versions of Fallopian Tube (Left)
Fallopian Tube (Right) May 28, 2025, 5:49 p.m. multiome-rna-atac 14 91339 NA 46054 NA Raw h5mu Processed h5mu NA All versions of Fallopian Tube (Right)
Fallopian Tube (Right) June 23, 2025, 7:09 p.m. rna-seq 38 34931 NA 15305 NA Raw H5AD Processed H5AD Shiny App All versions of Fallopian Tube (Right)
Heart June 23, 2025, 7:09 p.m. rna-seq 15 675772 21 22094 19 Raw H5AD Processed H5AD Shiny App All versions of Heart
Kidney (Left) June 23, 2025, 7:09 p.m. rna-seq 75 1522897 48 598799 48 Raw H5AD Processed H5AD Shiny App All versions of Kidney (Left)
Kidney (Right) June 23, 2025, 7:09 p.m. rna-seq 53 1803736 48 398963 48 Raw H5AD Processed H5AD Shiny App All versions of Kidney (Right)
Knee (Left) June 23, 2025, 7:09 p.m. rna-seq 2 21926 NA 12912 NA Raw H5AD Processed H5AD Shiny App All versions of Knee (Left)
Knee (Right) June 25, 2025, 3:17 p.m. rna-seq 11 128767 NA 86485 NA Raw H5AD Processed H5AD Shiny App All versions of Knee (Right)
Large Intestine Oct. 7, 2024, 3 p.m. atac 38 258178 NA 0 NA Raw h5mu NA All versions of Large Intestine
Large Intestine June 16, 2025, 3:09 p.m. codex 66 922074 NA 0 NA Raw H5AD NA All versions of Large Intestine
Large Intestine June 25, 2025, 3:17 p.m. rna-seq 45 172947 NA 96278 NA Raw H5AD Processed H5AD Shiny App All versions of Large Intestine
Liver June 25, 2025, 3:17 p.m. rna-seq 5 7916 NA 4433 NA Raw H5AD Processed H5AD Shiny App All versions of Liver
Lung (Right) June 25, 2025, 3:17 p.m. rna-seq 40 1166003 47 277488 47 Raw H5AD Processed H5AD Shiny App All versions of Lung (Right)
Lymph Node Nov. 7, 2024, 3:06 p.m. codex 64 2770708 NA 0 NA Raw H5AD NA All versions of Lymph Node
Lymph Node July 1, 2025, 7:02 p.m. CODEX 46 2167193 NA 0 NA Raw H5AD NA All versions of Lymph Node
Lymph Node May 19, 2025, 1:38 p.m. rna-seq 5 27383 NA 23722 NA Raw H5AD Processed H5AD Shiny App All versions of Lymph Node
Ovary (Left) May 28, 2025, 5:49 p.m. multiome-rna-atac 15 81924 NA 44972 NA Raw h5mu Processed h5mu NA All versions of Ovary (Left)
Ovary (Left) May 19, 2025, 1:38 p.m. rna-seq 43 139637 NA 81350 NA Raw H5AD Processed H5AD Shiny App All versions of Ovary (Left)
Ovary (Right) May 28, 2025, 5:49 p.m. multiome-rna-atac 18 85659 NA 41203 NA Raw h5mu Processed h5mu NA All versions of Ovary (Right)
Ovary (Right) May 19, 2025, 1:38 p.m. rna-seq 26 39799 NA 18006 NA Raw H5AD Processed H5AD Shiny App All versions of Ovary (Right)
Small Intestine June 16, 2025, 3:09 p.m. codex 67 1331626 NA 0 NA Raw H5AD NA All versions of Small Intestine
Small Intestine May 19, 2025, 1:38 p.m. rna-seq 43 146988 NA 102335 NA Raw H5AD Processed H5AD Shiny App All versions of Small Intestine
Spleen Nov. 7, 2024, 3:06 p.m. codex 65 3939679 NA 0 NA Raw H5AD NA All versions of Spleen
Spleen July 1, 2025, 7:02 p.m. CODEX 50 3288348 NA 0 NA Raw H5AD NA All versions of Spleen
Spleen May 19, 2025, 1:38 p.m. rna-seq 16 108929 NA 78030 NA Raw H5AD Processed H5AD Shiny App All versions of Spleen
Thymus Nov. 6, 2024, 3:26 p.m. codex 36 1525572 NA 0 NA Raw H5AD NA All versions of Thymus
Thymus July 1, 2025, 7:02 p.m. CODEX 26 1139097 NA 0 NA Raw H5AD NA All versions of Thymus
Uterus June 4, 2025, 2:50 p.m. multiome-rna-atac 15 112096 NA 40013 NA Raw h5mu Processed h5mu NA All versions of Uterus
Uterus June 23, 2025, 7:09 p.m. rna-seq 55 119689 NA 61046 NA Raw H5AD Processed H5AD Shiny App All versions of Uterus