Search ENCODE Experiments
encode_search_experimentsSearch ENCODE functional genomics experiments using filters like assay type, organism, tissue, cell line, or free text to find relevant datasets for analysis.
Instructions
Search ENCODE experiments with comprehensive filters.
Examples:
Find all Histone ChIP-seq on human pancreas tissue: assay_title="Histone ChIP-seq", organ="pancreas", biosample_type="tissue"
Find ATAC-seq on human brain: assay_title="ATAC-seq", organ="brain"
Find RNA-seq on GM12878 cell line: assay_title="RNA-seq", biosample_term_name="GM12878"
Find ChIP-seq targeting H3K27me3: assay_title="Histone ChIP-seq", target="H3K27me3"
Find all mouse liver experiments: organism="Mus musculus", organ="liver"
Free text search: search_term="CRISPR screen pancreatic"
Common assay_title values: "Histone ChIP-seq", "TF ChIP-seq", "ATAC-seq", "DNase-seq", "RNA-seq", "total RNA-seq", "WGBS", "Hi-C", "CUT&RUN", "CUT&Tag", "STARR-seq", "MPRA", "eCLIP", "CRISPR screen"
Common organ values: "pancreas", "liver", "brain", "heart", "kidney", "lung", "intestine", "skin of body", "blood", "spleen", "thymus"
biosample_type values: "tissue", "cell line", "primary cell", "in vitro differentiated cells", "organoid"
WHEN TO USE: Use as the primary entry point when users want to find experiments. Start with encode_get_facets if unsure what filters to use. RELATED TOOLS: encode_get_facets, encode_get_metadata, encode_search_files
Args: assay_title: Assay type (e.g., "Histone ChIP-seq", "ATAC-seq", "RNA-seq") organism: Species (default: "Homo sapiens"). Also: "Mus musculus" organ: Organ/tissue system (e.g., "pancreas", "brain", "liver") biosample_type: Sample classification ("tissue", "cell line", "primary cell", "organoid") biosample_term_name: Specific cell/tissue name (e.g., "GM12878", "HepG2", "pancreas") target: ChIP/CUT&RUN target (e.g., "H3K27me3", "CTCF", "p300") status: Data status (default: "released"). Also: "archived", "revoked" lab: Submitting lab name award: Funding project assembly: Genome assembly (e.g., "GRCh38", "mm10") replication_type: "isogenic", "anisogenic", or "unreplicated" life_stage: "embryonic", "postnatal", "child", "adult" sex: "male", "female", "mixed" treatment: Treatment name if perturbation experiment genetic_modification: Modification type ("CRISPR", "RNAi") perturbed: True for perturbation experiments only search_term: Free text search across all fields date_released_from: Start date (YYYY-MM-DD) for date range filter date_released_to: End date (YYYY-MM-DD) for date range filter limit: Max results to return (default 25, use larger for comprehensive searches) offset: Skip first N results (for pagination)
Returns: JSON with experiment results, total count, and pagination info.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| assay_title | No | ||
| organism | No | Homo sapiens | |
| organ | No | ||
| biosample_type | No | ||
| biosample_term_name | No | ||
| target | No | ||
| status | No | released | |
| lab | No | ||
| award | No | ||
| assembly | No | ||
| replication_type | No | ||
| life_stage | No | ||
| sex | No | ||
| treatment | No | ||
| genetic_modification | No | ||
| perturbed | No | ||
| search_term | No | ||
| date_released_from | No | ||
| date_released_to | No | ||
| limit | No | ||
| offset | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |