Cortexa research tool·genomics·epigenomics

ENCODE Search Rnaseq Experiments

Search ENCODE RNA-seq experiments by biosample (cell type or tissue), organism, and assay type (total RNA-seq, polyA plus RNA-seq, small RNA-seq, microRNA-seq). Returns experiment accessions, biosample summaries, lab names, and metadata from the ENCODE project. Use this to find ENCODE-curated RNA-seq data for specific cell lines or tissues.

Livelast probed 2026-04-30 23:07Z· 534msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 534ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "additionalProperties": false,
  "properties": {
    "assay_type": {
      "default": "total RNA-seq",
      "description": "RNA-seq assay type: 'total RNA-seq' (default, all RNA), 'polyA plus RNA-seq' (mRNA), 'small RNA-seq', 'microRNA-seq'. Aliases: 'total', 'polya', 'mirna', 'small'.",
      "type": "string"
    },
    "biosample": {
      "description": "Alias for biosample_term_name. Cell type or tissue (e.g., 'K562', 'liver').",
      "type": [
        "string",
        "null"
      ]
    },
    "biosample_term_name": {
      "description": "Biosample name from ENCODE ontology (e.g., 'K562', 'HepG2', 'GM12878', 'liver', 'brain'). Leave empty to search all biosamples.",
      "type": [
        "string",
        "null"
      ]
    },
    "cell_type": {
      "description": "Alias for biosample_term_name. Cell type (e.g., 'K562', 'HepG2', 'GM12878').",
      "type": [
        "string",
        "null"
      ]
    },
    "limit": {
      "default": 25,
      "description": "Maximum number of results to return (1-100).",
      "maximum": 100,
      "minimum": 1,
      "type": "integer"
    },
    "organism": {
      "default": "Homo sapiens",
      "description": "Organism scientific name (e.g., 'Homo sapiens', 'Mus musculus').",
      "type": "string"
    },
    "tissue": {
      "description": "Alias for biosample_term_name. Tissue type (e.g., 'liver', 'brain', 'heart').",
      "type": [
        "string",
        "null"
      ]
    }
  },
  "type": "object"
}

Examples (1)

Default ENCODE Search Rnaseq Experiments call

public-safeinput

{
  "limit": 3
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_ENCODE_search_rnaseq_experiments
Tool name: ENCODE_search_rnaseq_experiments
Added: 2026-04-30 22:47Z
Tags: tooluniverse

ENCODE Search Rnaseq Experiments

Livelast probed 2026-04-30 23:07Z· 534msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "additionalProperties": false, "properties": { "assay_type": { "default": "total RNA-seq", "description": "RNA-seq assay type: 'total RNA-seq' (default, all RNA), 'polyA plus RNA-seq' (mRNA), 'small RNA-seq', 'microRNA-seq'. Aliases: 'total', 'polya', 'mirna', 'small'.", "type": "string" }, "biosample": { "description": "Alias for biosample_term_name. Cell type or tissue (e.g., 'K562', 'liver').", "type": [ "string", "null" ] }, "biosample_term_name": { "description": "Biosample name from ENCODE ontology (e.g., 'K562', 'HepG2', 'GM12878', 'liver', 'brain'). Leave empty to search all biosamples.", "type": [ "string", "null" ] }, "cell_type": { "description": "Alias for biosample_term_name. Cell type (e.g., 'K562', 'HepG2', 'GM12878').", "type": [ "string", "null" ] }, "limit": { "default": 25, "description": "Maximum number of results to return (1-100).", "maximum": 100, "minimum": 1, "type": "integer" }, "organism": { "default": "Homo sapiens", "description": "Organism scientific name (e.g., 'Homo sapiens', 'Mus musculus').", "type": "string" }, "tissue": { "description": "Alias for biosample_term_name. Tissue type (e.g., 'liver', 'brain', 'heart').", "type": [ "string", "null" ] } }, "type": "object" }