Sequence Read Archive
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.
[{"category": "Organization", "contact_details": [{"contact_type": "email", "value": "sra@ncbi.nlm.nih.gov"}, {"contact_type": "url", "value": "https://www.ncbi.nlm.nih.gov/sra/docs/"}], "label": "NCBI SRA"}]
[{"category": "GraphicalInterface", "description": "Main SRA search and browse interface for studies, experiments, runs, and associated metadata.", "format": "http", "id": "sra.portal", "name": "SRA Portal", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "sra"}], "product_url": "https://www.ncbi.nlm.nih.gov/sra"}, {"category": "DocumentationProduct", "description": "Official SRA documentation covering submission, search, download, cloud usage, and archive behavior.", "format": "http", "id": "sra.docs", "name": "SRA Documentation", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "sra"}], "product_url": "https://www.ncbi.nlm.nih.gov/sra/docs/"}, {"category": "GraphicalInterface", "description": "SRA Run Selector interface for exporting run-level metadata tables and filtering search results.", "format": "http", "id": "sra.run_selector", "name": "SRA Run Selector", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "sra"}], "product_url": "https://www.ncbi.nlm.nih.gov/Traces/study/"}, {"category": "Product", "description": "Latest human gene-level ARCHS4 expression matrix in HDF5 format using Ensembl 107 annotations", "format": "hdf5", "id": "archs4.human.gene_counts", "name": "ARCHS4 Human Gene Counts", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "archs4"}, {"relation_type": "prov:hadPrimarySource", "source": "geo"}, {"relation_type": "prov:hadPrimarySource", "source": "sra"}, {"relation_type": "prov:wasDerivedFrom", "source": "ensembl"}], "product_file_size": 61899310543, "product_url": "https://s3.dev.maayanlab.cloud/archs4/files/human_gene_v2.latest.h5"}, {"category": "Product", "description": "Latest mouse gene-level ARCHS4 expression matrix in HDF5 format using Ensembl 107 annotations", "format": "hdf5", "id": "archs4.mouse.gene_counts", "name": "ARCHS4 Mouse Gene Counts", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "archs4"}, {"relation_type": "prov:hadPrimarySource", "source": "geo"}, {"relation_type": "prov:hadPrimarySource", "source": "sra"}, {"relation_type": "prov:wasDerivedFrom", "source": "ensembl"}], "product_file_size": 49065676268, "product_url": "https://s3.dev.maayanlab.cloud/archs4/files/mouse_gene_v2.latest.h5"}, {"category": "Product", "description": "Latest human transcript-level ARCHS4 expression matrix in HDF5 format using Ensembl 107 annotations", "format": "hdf5", "id": "archs4.human.transcript_counts", "name": "ARCHS4 Human Transcript Counts", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "archs4"}, {"relation_type": "prov:hadPrimarySource", "source": "geo"}, {"relation_type": "prov:hadPrimarySource", "source": "sra"}, {"relation_type": "prov:wasDerivedFrom", "source": "ensembl"}], "product_file_size": 192013010374, "product_url": "https://s3.dev.maayanlab.cloud/archs4/files/human_transcript_v2.latest.h5"}, {"category": "Product", "description": "Latest mouse transcript-level ARCHS4 expression matrix in HDF5 format using Ensembl 107 annotations", "format": "hdf5", "id": "archs4.mouse.transcript_counts", "name": "ARCHS4 Mouse Transcript Counts", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "archs4"}, {"relation_type": "prov:hadPrimarySource", "source": "geo"}, {"relation_type": "prov:hadPrimarySource", "source": "sra"}, {"relation_type": "prov:wasDerivedFrom", "source": "ensembl"}], "product_file_size": 113637723557, "product_url": "https://s3.dev.maayanlab.cloud/archs4/files/mouse_transcript_v2.latest.h5"}, {"category": "Product", "description": "Collection page for ARCHS4 Zoo downloads covering selected additional species beyond human and mouse", "format": "hdf5", "id": "archs4.zoo", "name": "ARCHS4 Zoo Downloads", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "archs4"}, {"relation_type": "prov:hadPrimarySource", "source": "geo"}, {"relation_type": "prov:hadPrimarySource", "source": "sra"}, {"relation_type": "prov:wasDerivedFrom", "source": "ensembl"}], "product_url": "https://archs4.org/zoo"}, {"category": "Product", "description": "Computational pipeline for gathering publicly available RNA-seq data, aligning reads, performing quality control, computing iModulons using independent component analysis, and formatting dashboard files. Enables users to generate their own iModulon decompositions from transcriptomic datasets.", "format": "http", "id": "imodulondb.imodulonminer", "name": "iModulonMiner Pipeline", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "imodulondb"}], "product_url": "https://github.com/SBRG/iModulonMiner", "secondary_source": [{"relation_type": "prov:wasDerivedFrom", "source": "sra"}]}, {"category": "Product", "description": "Modulome workflow for scraping publicly available data for an organism, aligning reads, quality control, and computing iModulons. Used to expand iModulonDB across the prokaryotic evolutionary tree by processing data from the Sequence Read Archive.", "format": "http", "id": "imodulondb.modulome_workflow", "name": "Modulome Workflow", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "imodulondb"}], "product_url": "https://github.com/avsastry/modulome-workflow", "secondary_source": [{"relation_type": "prov:wasDerivedFrom", "source": "sra"}]}, {"category": "Product", "description": "Downloadable transcriptomic datasets and iModulon decompositions for 15 organisms including E. coli, B. subtilis, S. aureus, M. tuberculosis, P. aeruginosa, P. putida, and others. Includes gene expression matrices, iModulon activity matrices, gene weights, and metadata for over 9500 expression profiles from 525 studies.", "format": "mixed", "id": "imodulondb.datasets", "name": "iModulonDB Datasets", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "imodulondb"}], "product_url": "https://imodulondb.org/", "secondary_source": [{"relation_type": "prov:wasInformedBy", "source": "biocyc"}, {"relation_type": "prov:wasDerivedFrom", "source": "sra"}, {"relation_type": "prov:wasInformedBy", "source": "string"}]}]
{"activity_status": "active", "category": "DataSource", "contacts": [{"category": "Organization", "contact_details": [{"contact_type": "email", "value": "sra@ncbi.nlm.nih.gov"}, {"contact_type": "url", "value": "https://www.ncbi.nlm.nih.gov/sra/docs/"}], "label": "NCBI SRA"}], "creation_date": "2026-05-21T00:00:00Z", "description": "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.", "domains": ["genomics", "biomedical", "organisms"], "homepage_url": "https://www.ncbi.nlm.nih.gov/sra", "id": "sra", "last_modified_date": "2026-05-22T00:00:00Z", "layout": "resource_detail", "name": "Sequence Read Archive", "products": [{"category": "GraphicalInterface", "description": "Main SRA search and browse interface for studies, experiments, runs, and associated metadata.", "format": "http", "id": "sra.portal", "name": "SRA Portal", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "sra"}], "product_url": "https://www.ncbi.nlm.nih.gov/sra"}, {"category": "DocumentationProduct", "description": "Official SRA documentation covering submission, search, download, cloud usage, and archive behavior.", "format": "http", "id": "sra.docs", "name": "SRA Documentation", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "sra"}], "product_url": "https://www.ncbi.nlm.nih.gov/sra/docs/"}, {"category": "GraphicalInterface", "description": "SRA Run Selector interface for exporting run-level metadata tables and filtering search results.", "format": "http", "id": "sra.run_selector", "name": "SRA Run Selector", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "sra"}], "product_url": "https://www.ncbi.nlm.nih.gov/Traces/study/"}, {"category": "Product", "description": "Latest human gene-level ARCHS4 expression matrix in HDF5 format using Ensembl 107 annotations", "format": "hdf5", "id": "archs4.human.gene_counts", "name": "ARCHS4 Human Gene Counts", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "archs4"}, {"relation_type": "prov:hadPrimarySource", "source": "geo"}, {"relation_type": "prov:hadPrimarySource", "source": "sra"}, {"relation_type": "prov:wasDerivedFrom", "source": "ensembl"}], "product_file_size": 61899310543, "product_url": "https://s3.dev.maayanlab.cloud/archs4/files/human_gene_v2.latest.h5"}, {"category": "Product", "description": "Latest mouse gene-level ARCHS4 expression matrix in HDF5 format using Ensembl 107 annotations", "format": "hdf5", "id": "archs4.mouse.gene_counts", "name": "ARCHS4 Mouse Gene Counts", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "archs4"}, {"relation_type": "prov:hadPrimarySource", "source": "geo"}, {"relation_type": "prov:hadPrimarySource", "source": "sra"}, {"relation_type": "prov:wasDerivedFrom", "source": "ensembl"}], "product_file_size": 49065676268, "product_url": "https://s3.dev.maayanlab.cloud/archs4/files/mouse_gene_v2.latest.h5"}, {"category": "Product", "description": "Latest human transcript-level ARCHS4 expression matrix in HDF5 format using Ensembl 107 annotations", "format": "hdf5", "id": "archs4.human.transcript_counts", "name": "ARCHS4 Human Transcript Counts", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "archs4"}, {"relation_type": "prov:hadPrimarySource", "source": "geo"}, {"relation_type": "prov:hadPrimarySource", "source": "sra"}, {"relation_type": "prov:wasDerivedFrom", "source": "ensembl"}], "product_file_size": 192013010374, "product_url": "https://s3.dev.maayanlab.cloud/archs4/files/human_transcript_v2.latest.h5"}, {"category": "Product", "description": "Latest mouse transcript-level ARCHS4 expression matrix in HDF5 format using Ensembl 107 annotations", "format": "hdf5", "id": "archs4.mouse.transcript_counts", "name": "ARCHS4 Mouse Transcript Counts", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "archs4"}, {"relation_type": "prov:hadPrimarySource", "source": "geo"}, {"relation_type": "prov:hadPrimarySource", "source": "sra"}, {"relation_type": "prov:wasDerivedFrom", "source": "ensembl"}], "product_file_size": 113637723557, "product_url": "https://s3.dev.maayanlab.cloud/archs4/files/mouse_transcript_v2.latest.h5"}, {"category": "Product", "description": "Collection page for ARCHS4 Zoo downloads covering selected additional species beyond human and mouse", "format": "hdf5", "id": "archs4.zoo", "name": "ARCHS4 Zoo Downloads", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "archs4"}, {"relation_type": "prov:hadPrimarySource", "source": "geo"}, {"relation_type": "prov:hadPrimarySource", "source": "sra"}, {"relation_type": "prov:wasDerivedFrom", "source": "ensembl"}], "product_url": "https://archs4.org/zoo"}, {"category": "Product", "description": "Computational pipeline for gathering publicly available RNA-seq data, aligning reads, performing quality control, computing iModulons using independent component analysis, and formatting dashboard files. Enables users to generate their own iModulon decompositions from transcriptomic datasets.", "format": "http", "id": "imodulondb.imodulonminer", "name": "iModulonMiner Pipeline", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "imodulondb"}], "product_url": "https://github.com/SBRG/iModulonMiner", "secondary_source": [{"relation_type": "prov:wasDerivedFrom", "source": "sra"}]}, {"category": "Product", "description": "Modulome workflow for scraping publicly available data for an organism, aligning reads, quality control, and computing iModulons. Used to expand iModulonDB across the prokaryotic evolutionary tree by processing data from the Sequence Read Archive.", "format": "http", "id": "imodulondb.modulome_workflow", "name": "Modulome Workflow", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "imodulondb"}], "product_url": "https://github.com/avsastry/modulome-workflow", "secondary_source": [{"relation_type": "prov:wasDerivedFrom", "source": "sra"}]}, {"category": "Product", "description": "Downloadable transcriptomic datasets and iModulon decompositions for 15 organisms including E. coli, B. subtilis, S. aureus, M. tuberculosis, P. aeruginosa, P. putida, and others. Includes gene expression matrices, iModulon activity matrices, gene weights, and metadata for over 9500 expression profiles from 525 studies.", "format": "mixed", "id": "imodulondb.datasets", "name": "iModulonDB Datasets", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "imodulondb"}], "product_url": "https://imodulondb.org/", "secondary_source": [{"relation_type": "prov:wasInformedBy", "source": "biocyc"}, {"relation_type": "prov:wasDerivedFrom", "source": "sra"}, {"relation_type": "prov:wasInformedBy", "source": "string"}]}], "synonyms": ["SRA", "Sequence Read Archive"]}