HTAN Phase 1 metadata snapshot: Release 7

A parquet snapshot of the Human Tumor Atlas Network (HTAN) Phase 1 open-access metadata, clinical and provenance tables, Release 7. It has 78 tables and 821,773 rows, 19.8 MB as zstd parquet.

It was exported from ISB-CGC's public BigQuery dataset (isb-cgc-bq.HTAN_versioned, pinned *_r7 tables) so the data can be queried without a Google Cloud account or billing, from DuckDB, R, Python or this page's viewer.

The snapshot is the data index for the R/Bioconductor client HTAN, which reads manifest.json from this repository (pinned to the r7 tag), verifies each file's sha256, and serves the tables as DuckDB views and dbplyr tibbles.

-- DuckDB
SELECT * FROM 'hf://datasets/seandavis/htan@r7/biospecimen.parquet' LIMIT 10;

Contents

• manifest.json: release, build date, source table, row count, byte size, sha256 and column descriptions for every table.
• One parquet file per table:

Table	Category	Rows
10xvisium_spatialtranscriptomics_auxiliaryfiles_metadata	metadata	465
10xvisium_spatialtranscriptomics_scRNAseq_level1_metadata	metadata	794
10xvisium_spatialtranscriptomics_scRNAseq_level2_metadata	metadata	223
10xvisium_spatialtranscriptomics_scRNAseq_level3_metadata	metadata	1,264
10xvisium_spatialtranscriptomics_scRNAseq_level4_metadata	metadata	175
10xxenium_spatialtranscriptomics_experiment_metadata	metadata	33
ScDNAseq_level1_metadata	metadata	1,774
ScDNAseq_level2_metadata	metadata	1,271
Slide_seqLevel1_metadata	metadata	7
Slide_seqLevel2_metadata	metadata	47
Slide_seqLevel3_metadata	metadata	329
accessory_manifest	metadata	5
biospecimen	clinical_biospecimen_data	13,105
bulkMethylationseq_level1_metadata	metadata	80
bulkMethylationseq_level2_metadata	metadata	51
bulkRNAseq_level1_metadata	metadata	4,134
bulkRNAseq_level2_metadata	metadata	1,922
bulkRNAseq_level3_metadata	metadata	640
bulkWES_level1_metadata	metadata	7,033
bulkWES_level2_metadata	metadata	1,613
bulkWES_level3_metadata	metadata	1,014
clinical_tier1_demographics	clinical_biospecimen_data	2,805
clinical_tier1_diagnosis	clinical_biospecimen_data	2,300
clinical_tier1_exposure	clinical_biospecimen_data	2,004
clinical_tier1_familyhistory	clinical_biospecimen_data	2,284
clinical_tier1_followup	metadata	2,167
clinical_tier1_moleculartest	clinical_biospecimen_data	4,700
clinical_tier1_therapy	clinical_biospecimen_data	3,337
clinical_tier2	clinical_biospecimen_data	359
clinical_tier3_brain	clinical_biospecimen_data	82
clinical_tier3_breast	clinical_biospecimen_data	129
clinical_tier3_colorectal	clinical_biospecimen_data	304
clinical_tier3_lung	clinical_biospecimen_data	77
clinical_tier3_melanoma	clinical_biospecimen_data	61
dataFileSynapseID_to_BigQueryTableID_map	metadata	1,610
electron_microscopy_level1_metadata	metadata	74,252
electron_microscopy_level2_metadata	metadata	36,073
electron_microscopy_level3_metadata	metadata	32
electron_microscopy_level4_metadata	metadata	41
exseq_minimal	metadata	21,153
gc_drs_map	metadata	66,891
hiCseq_level1_metadata	metadata	66
hiCseq_level2_metadata	metadata	34
hiCseq_level3_metadata	metadata	2
id_provenance	metadata	464,304
imaging_channel_metadata	metadata	23,972
imaging_level1_metadata	metadata	16
imaging_level2_metadata	metadata	27,079
imaging_level3_segmentation_metadata	metadata	4,628
imaging_level4_metadata	metadata	3,539
lipidomics_metadata	metadata	84
massSpectrometry_level1_metadata	metadata	1,187
massSpectrometry_level3_metadata	metadata	28
massSpectrometry_level4_metadata	metadata	28
metabolomics_metadata	metadata	176
nanostring_spatialtranscriptomics_geomx_level1_metadata	metadata	239
nanostring_spatialtranscriptomics_geomx_level3_metadata	metadata	53
other_assay_metadata	metadata	122
participantVitalStatusUpdate	clinical_biospecimen_data	2
phase1_longitudinal_data	metadata	7,620
proteomics_metadata	metadata	392
publication_manifest_metadata	metadata	1
rppa_level2_metadata	metadata	26
rppa_level3_metadata	metadata	26
rppa_level4_metadata	metadata	26
scATACseq_level1_metadata	metadata	2,548
scATACseq_level2_metadata	metadata	344
scATACseq_level3_metadata	metadata	1,006
scATACseq_level4_metadata	metadata	218
scRNAseq_level1_metadata	metadata	15,201
scRNAseq_level2_metadata	metadata	5,755
scRNAseq_level3_metadata	metadata	3,705
scRNAseq_level4_metadata	metadata	857
schema	metadata	1,072
srrs_biospecimen	clinical_biospecimen_data	286
srrs_clinical_tier2	clinical_biospecimen_data	16
srrs_imaging_level2_metadata	metadata	143
tissueOrOrganOfOrigin_to_wholeOrgan_mapping	metadata	332

These are metadata only. Data files (FASTQ, images, h5ad/rds, cell tables) stay with HTAN: open imaging is in the CRDC General Commons, and processed files are on Synapse. The HTAN R package resolves and downloads them.

Versioning

Each HTAN release is a git tag on this repository (r7 = HTAN Phase 1 Release 7, built 2026-10-14T11:53:18Z). Phase 1 is frozen at Release 7. Phase 2 data will be published under its own tag when its data model stabilizes.

Provenance, attribution and terms

• Source: HTAN Data Coordinating Center releases, as loaded into BigQuery by ISB-CGC (isb-cgc-bq.HTAN_versioned).
• Terms: HTAN releases these tables as open access. I haven't found an explicit license for the HTAN metadata. HTAN's open Level 2 imaging in the CRDC General Commons and IDC is distributed under CC BY 4.0, but that statement covers the images, not these tables. Until HTAN states terms, treat this snapshot as subject to HTAN's open-access data use and publication guidelines: cite HTAN, and don't attempt re-identification. See humantumoratlas.org. Column descriptions come from the HTAN data model and ISB-CGC.
• If the HTAN DCC or ISB-CGC asks for changes to this mirror, open a discussion on this repository or email seandavi@gmail.com.
• Not an official HTAN or ISB-CGC distribution. This is a convenience mirror maintained by Sean Davis (Bioconductor, U24CA289073). For the authoritative data, use the HTAN Data Portal.

Citation

Rozenblatt-Rosen O, et al. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell 2020;181(2):236–249. doi:10.1016/j.cell.2020.03.053. PMID: 32302568