is a Data Source.
The Sequence Read Archive (SRA) is NCBI's public archive of high-throughput sequencing data and part of the International Nucleotide Sequence Database Collaboration, providing searchable access to raw sequence runs, metadata, cloud delivery, and download tooling.
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| sra.portal | SRA Portal | sra | Graphical Interface | http | Main SRA search and browse interface ... |
| sra.docs | SRA Documentation | docs | Documentation | http | Official SRA documentation covering s... |
| sra.run_selector | SRA Run Selector | study | Graphical Interface | http | SRA Run Selector interface for export... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| archs4.human.gene_counts | ARCHS4 Human Gene Counts | human_gene_v2.latest.h5 (57.6 GB) | Product | hdf5 | had primary source | Latest human gene-level ARCHS4 expres... |
| archs4.mouse.gene_counts | ARCHS4 Mouse Gene Counts | mouse_gene_v2.latest.h5 (45.7 GB) | Product | hdf5 | had primary source | Latest mouse gene-level ARCHS4 expres... |
| archs4.human.transcript_counts | ARCHS4 Human Transcript Counts | human_transcript_v2.latest.h5 (178.8 GB) | Product | hdf5 | had primary source | Latest human transcript-level ARCHS4 ... |
| archs4.mouse.transcript_counts | ARCHS4 Mouse Transcript Counts | mouse_transcript_v2.latest.h5 (105.8 GB) | Product | hdf5 | had primary source | Latest mouse transcript-level ARCHS4 ... |
| archs4.zoo | ARCHS4 Zoo Downloads | zoo | Product | hdf5 | had primary source | Collection page for ARCHS4 Zoo downlo... |
| imodulondb.imodulonminer | iModulonMiner Pipeline | iModulonMiner | Product | http | was derived from | Computational pipeline for gathering ... |
| imodulondb.modulome_workflow | Modulome Workflow | modulome-workflow | Product | http | was derived from | Modulome workflow for scraping public... |
| imodulondb.datasets | iModulonDB Datasets | imodulondb.org | Product | mixed | was derived from | Downloadable transcriptomic datasets ... |
| nde.graph | NIAID Data Ecosystem KG (graph) | nde | Graph | ttl | was influenced by | RDF (Turtle) knowledge graph of the N... |
| chip-atlas.portal | ChIP-Atlas Web Portal | chip-atlas.org | Graphical Interface | http | had primary source | ChIP-Atlas web portal with the Peak B... |
| chip-atlas.experimentlist | ChIP-Atlas experimentList.tab | experimentList.tab (342.8 MB) | Product | tsv | had primary source | Metadata table describing every ChIP-... |
| chip-atlas.peaks.each | ChIP-Atlas Per-Experiment Peak Calls and Coverage | data | Product | mixed | had primary source | Peak calls (MACS2, BED4 and BigBed) a... |
| chip-atlas.peaks.assembled | ChIP-Atlas Assembled Peak-call Data | Oth.ALL.05.GATA2.AllCell.bed (607.9 MB) | Product | txt | had primary source | Assembled BED9 peak-call files used i... |
| chip-atlas.peaks.light | ChIP-Atlas All Peaks (Light) | allPeaks_light.hg38.05.bed.gz (19.9 GB) | Product | txt | had primary source | Lighter version of all peak-call data... |
| chip-atlas.targetgenes | ChIP-Atlas Target Genes | POU5F1.5.tsv (2.5 MB) | Product | tsv | had primary source | Predicted target genes of each transc... |
| chip-atlas.colocalization | ChIP-Atlas Colocalization | POU5F1.Pluripotent_stem_cell.tsv (264.1 KB) | Product | tsv | had primary source | Colocalization scores between pairs o... |
| ddbj.dra | DDBJ Sequence Read Archive (DRA) | dra | Product | mixed | was influenced by | DDBJ Sequence Read Archive (DRA) down... |
| gtrd.downloads | GTRD Downloads | current | Product | http | was derived from | GTRD bulk download directory with pla... |
| gtrd.chip-seq_peaks | GTRD ChIP-seq Peaks | chip-seq | Product | http | was derived from | Per-species archives of transcription... |
SRA is the largest public repository of high-throughput sequencing data and serves as NCBI’s contribution to the INSDC sequence archive ecosystem. It supports archival storage, search, metadata export, toolkit-based download, cloud access patterns, and controlled-access handling for sensitive human data via dbGaP-linked workflows.
The ARCHS4 products listed here are downstream matrices built from SRA and GEO RNA-seq inputs. They remain attached as derived products because SRA is a direct upstream source of the sequence data used in those uniformly processed expression releases.
Created: May 21, 2026 | Last modified: September 23, 2026