/sra/experiments/search

POST /api/sra/experiments/search

Price: 20 credits

Search SRA sequencing experiments by query and library filters

How to use it

Searches the Sequence Read Archive at experiment level - one row per sequencing library, with its runs nested. The library facets are the useful ones: `strategies` says what the experiment measures (RNA-Seq, WGS, ATAC-seq), `sources` says what material it came from, and the single-cell distinction lives in `sources` rather than in `strategies`. `accession` matches at any level, so a study accession returns every experiment under it. A misspelt bracket tag inside `term` is not rejected - it falls through to a free-text match and quietly widens the result set, so prefer the structured fields. Results come back in the archive's own order; there is no ranking to request.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• term string nullable — Free-text query in Entrez syntax. Supports bracketed field tags (human[Organism], RNA-Seq[Strategy]), boolean AND/OR/NOT and year ranges (2018:2022[PDAT]). Combined with AND against every structured filter below (examples: "single cell brain", "tumor AND RNA-Seq")
• count integer required — Number of experiments to return (min: 1; max: 5000)
• offset integer — How many matches to skip before the returned page, for walking past a single call's ceiling (default: 0; min: 0; max: 100000)
• organism string nullable — Filter by source organism, scientific or common name (examples: "Homo sapiens", "human")
• experiment_title string nullable — Filter by words in the experiment title (examples: "RNA-Seq")
• author string nullable — Filter by submitting author (examples: "Smith J")
• accession string nullable — Filter by an SRA accession of any level (experiment, study, sample or run) (examples: "SRX1234567", "SRP011949")
• bioproject string nullable — Filter by the BioProject the experiments belong to (examples: "PRJNA157243")
• biosample string nullable — Filter by the BioSample the library was built from (examples: "SAMN03898702")
• platforms array nullable — Filter by sequencing platform (any-of) (one of: "illumina", "oxford_nanopore", "pacbio_smrt", "ion_torrent", "bgiseq", "dnbseq", "capillary", "abi_solid", "ls454", "helicos", "complete_genomics", "element", "ultima", "genapsys", "tapestri", "vela_diagnostics", "singular_genomics")
• strategies array nullable — Filter by what the library was built to measure (any-of) (one of: "wgs", "wga", "wxs", "rna_seq", "mirna_seq", "ncrna_seq", "ssrna_seq", "atac_seq", "chip_seq", "bisulfite_seq", "amplicon", "clone", "poolclone", "cloneend", "finishing", "mnase_seq", "dnase_hypersensitivity", "est", "fl_cdna", "cts", "mre_seq", "medip_seq", "mbd_seq", "tn_seq", "validation", "faire_seq", "selex", "rip_seq", "chia_pet", "synthetic_long_read", "targeted_capture", "tethered_chromatin_conformation_capture", "hi_c", "ribo_seq", "other")
• sources array nullable — Filter by the kind of material the library came from (any-of) (one of: "genomic", "transcriptomic", "metagenomic", "metatranscriptomic", "synthetic", "viral_rna", "genomic_single_cell", "transcriptomic_single_cell", "other")
• selections array nullable — Filter by the method used to select the molecules that were sequenced (any-of) (one of: "random", "pcr", "random_pcr", "rt_pcr", "hmpr", "mf", "mda", "msll", "cdna", "chip", "mnase", "dnase", "hybrid_selection", "reduced_representation", "restriction_digest", "methylcytidine_antibody", "mbd2_protein_methyl_cpg_binding_domain", "cage", "race", "size_fractionation", "padlock_probes_capture", "inverse_rrna", "oligo_dt", "polya", "repeat_fractionation", "unspecified", "other")
• layouts array nullable — Filter by whether reads are paired-end or single-end (any-of) (one of: "paired", "single")
• access array nullable — Filter by whether the reads themselves are openly downloadable or require dbGaP authorisation (any-of) (one of: "public", "controlled")
• mindate string nullable — Start of the date range (YYYY, YYYY/MM or YYYY/MM/DD); used with maxdate (examples: "2024")
• maxdate string nullable — End of the date range (YYYY, YYYY/MM or YYYY/MM/DD); used with mindate (examples: "2024")
• datetype string — Which date the range applies to (default: "pdat"; one of: "pdat", "mdat")

Response

• @type string (default: "SraExperiment")
• id string required
• accession string (default: "")
• experiment_title string (default: "")
• name string (default: "")
• version string (default: "")
• status string (default: "")
• platform string (default: "")
• instrument_model string (default: "")
• run_count integer nullable
• spot_count integer nullable
• base_count integer nullable
• size integer nullable
• cluster_name string (default: "")
• is_load_done boolean (default: false)
• has_static_data boolean (default: false)
• has_filtered_data boolean (default: false)
• submitter_accession string (default: "")
• center_name string (default: "")
• contact_name string (default: "")
• lab_name string (default: "")
• study_accession string (default: "")
• study_title string (default: "")
• sample_accession string (default: "")
• sample_name string (default: "")
• organism string (default: "")
• common_name string (default: "")
• taxid string (default: "")
• bioproject_accession string (default: "")
• biosample_accession string (default: "")
• library_name string (default: "")
• library_strategy string (default: "")
• library_source string (default: "")
• library_selection string (default: "")
• library_layout string (default: "")
• library_construction_protocol string (default: "")
• nominal_length integer nullable
• nominal_sdev number nullable
• controlled_access_study string (default: "")
• controlled_access_consent string (default: "")
• runs array (default: [])
  • @type string (default: "SraRun")
  • accession string required
  • spot_count integer nullable
  • base_count integer nullable
  • cluster_name string (default: "")
  • is_public boolean (default: false)
  • is_load_done boolean (default: false)
  • is_unavailable boolean (default: false)
  • has_static_data boolean (default: false)
  • has_filtered_data boolean (default: false)
  • url string (default: "")
• created_date string (default: "")
• updated_date string (default: "")
• url string (default: "")

Errors

• 422 — The request body did not validate Check the fields against this schema. A URN with the wrong prefix is the most common cause.
• 408 — The request ran past its time limit Raise `timeout` in the request body, up to the maximum this endpoint documents. Lowering `count` or turning off the `with_*` flags also helps, because less work finishes sooner.
• 412 — The entity was not found, or a precondition failed Retrying will not help: either the entity does not exist, or the input points at a different one.
• 429 — Too many requests: a rate limit or a usage window is exhausted When the response carries an X-Retry-After header, wait that many seconds and retry: the same number is in the body as `detail.retry_after`, and the limit clears once that window passes. The message in the body names the limit that was hit.
• 500 — Something broke on our side Retrying will not help. If it keeps happening, send us the X-Request-ID from the response headers.
• 529 — Rate limit reached, or the endpoint is overloaded Wait at least 30 seconds, then retry.

Response headers

• X-Error — Error message text (present only on error)
• X-Request-ID — Unique request identifier
• X-Execution-Time — Execution time in seconds
• X-Result-Count — How many records the body carries. 0 means an empty result, which is a normal answer and not by itself an error. A non-zero count can come back together with X-Error when the failure happened partway through — read this header and X-Error independently.
• X-Total-Available-Results — How many records exist for this query, when the endpoint can say. On a `dry_run` request this is the answer and the body is empty. It saturates: the endpoint's documented maximum means 'at least that many', any smaller number is exact.
• X-Warning — Present when the request body carried keys this endpoint does not document. They were ignored, so any filter you meant to apply through them did not apply. Check the spelling against this schema and retry.
• X-Retry-After — Seconds to wait before retrying. Present only on 429.