Cortexa research tool·genomics·encode

ENCODE Search Experiments

Search ENCODE functional genomics experiments (e.g., ChIP-seq, ATAC-seq, RNA-seq) by assay type, target protein, organism, or status. Returns experiment accessions, descriptions, and metadata. Use this to discover datasets for specific assays, transcription factors, or cell types. Find experiment accessions to use with ENCODE_get_experiment for detailed information or ENCODE_list_files for downloading data files.

Livelast probed 2026-04-30 23:07Z· 878msCortexa

Status

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

Last probed: 1d ago
Last success: 1d ago
Last latency: 878ms

Schema

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

{
  "properties": {
    "assay_title": {
      "description": "Assay name filter (e.g., 'TF ChIP-seq', 'Histone ChIP-seq', 'ATAC-seq', 'RNA-seq', 'Hi-C'). Leave empty to search all assays. Use 'TF ChIP-seq' for transcription factor binding experiments.",
      "type": "string"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of results to return (1–100).",
      "maximum": 100,
      "minimum": 1,
      "type": "integer"
    },
    "organism": {
      "description": "Organism filter — maps to ENCODE's organism scientific name field (e.g., 'Homo sapiens', 'Mus musculus', 'Drosophila melanogaster').",
      "type": "string"
    },
    "status": {
      "default": "released",
      "description": "Record status filter. Use 'released' for public data (default), 'archived' for older data.",
      "type": "string"
    },
    "target": {
      "description": "Target protein/factor filter (e.g., 'CTCF', 'H3K4me3', 'POLR2A'). Use for TF ChIP-seq experiments.",
      "type": "string"
    }
  },
  "type": "object"
}

Examples (1)

Default ENCODE Search 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_experiments
Tool name: ENCODE_search_experiments
Added: 2026-04-30 22:47Z
Tags: tooluniverse

ENCODE Search Experiments

Livelast probed 2026-04-30 23:07Z· 878msCortexa

Schema

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

{ "properties": { "assay_title": { "description": "Assay name filter (e.g., 'TF ChIP-seq', 'Histone ChIP-seq', 'ATAC-seq', 'RNA-seq', 'Hi-C'). Leave empty to search all assays. Use 'TF ChIP-seq' for transcription factor binding experiments.", "type": "string" }, "limit": { "default": 10, "description": "Maximum number of results to return (1–100).", "maximum": 100, "minimum": 1, "type": "integer" }, "organism": { "description": "Organism filter — maps to ENCODE's organism scientific name field (e.g., 'Homo sapiens', 'Mus musculus', 'Drosophila melanogaster').", "type": "string" }, "status": { "default": "released", "description": "Record status filter. Use 'released' for public data (default), 'archived' for older data.", "type": "string" }, "target": { "description": "Target protein/factor filter (e.g., 'CTCF', 'H3K4me3', 'POLR2A'). Use for TF ChIP-seq experiments.", "type": "string" } }, "type": "object" }