Here's an overview of HTAN data:
Database snapshot: htan_2026_01_08 — 221,285 files across 2,890 participants
The largest data contributors are:
| Atlas | Files | Participants |
|---|---|---|
| HTAN OHSU | 116,657 | 33 |
| HTAN HTAPP | 41,631 | 205 |
| HTAN DFCI | 17,560 | 156 |
| HTAN Duke | 7,035 | 828 |
| HTAN WUSTL | 7,176 | 287 |
| HTAN Stanford | 5,913 | 40 |
| HTAN MSK | 5,381 | 202 |
| HTAN BU | 5,319 | 484 |
Imaging dominates by file count:
- Electron Microscopy — 110,398 files
- MERFISH — 18,626
- ExSEQ — 21,156
- CyCIF / CODEX / MxIF / MIBI / IMC — multiplexed imaging
Single-cell genomics:
- scRNA-seq — 25,533 files
- scATAC-seq — 4,116
- scDNA-seq — 3,056
Spatial transcriptomics:
- 10X Visium — 2,921
- Slide-seq — 383
- NanoString GeoMx DSP — 395
- 10X Xenium ISS — 33
Bulk genomics:
- Bulk DNA — 9,660
- Bulk RNA-seq — 6,696
Proteomics / metabolomics:
- LC-MS/MS & LC-MS3 — 972
- RPPA — 78
| Organ | Files |
|---|---|
| Breast | 157,186 |
| Skin | 10,878 |
| Colorectal | 10,847 |
| Brain | 10,601 |
| Lung | 6,960 |
| Pancreas | 2,291 |
| Bone Marrow | 1,228 |
| Ovary | 945 |
Plus liver, kidney, cervix, stomach, head & neck, and more.
7 queryable tables: files, cases, demographics, diagnosis, specimen, atlases, and publication_manifest.
- Find specific files:
uv run htan query portal files --organ Breast --assay "scRNA-seq" - Query clinical data:
uv run htan query portal demographics --atlas "HTAN OHSU" - Search publications:
uv run htan pubs search --keyword "spatial transcriptomics" - Deep metadata queries via BigQuery: file sizes, cell counts, library methods
Let me know if you'd like to drill into a specific atlas, organ, or assay type!