{
"@context": "/terms/",
"@id": "/configuration-files/IGVFFI2982KSVM/",
"@type": [
"ConfigurationFile",
"File",
"Item"
],
"accession": "IGVFFI2982KSVM",
"aliases": [
"jesse-engreitz:seqspecfile_rna_CRUDO_TAPseq_Auxin6hrs-Rep2-S4"
],
"assay_titles": [
"TAP-seq"
],
"audit": {},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"content_md5sum": "613c506bfeb3294c9a71cb8813c5b228",
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:52.002958+00:00",
"file_format": "yaml",
"file_set": {
"@id": "/measurement-sets/IGVFDS8403DDLC/",
"accession": "IGVFDS8403DDLC",
"file_set_type": "experimental data",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8511JOMW/",
"accession": "IGVFSM8511JOMW",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released",
"summary": "AID system targeting RAD21"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"status": "released",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"status": "released",
"summary": "mixed CRISPR TAP-seq integrating a guide (sgRNA) library targeting accessible genome regions in 29 genomic loci"
},
"file_size": 1045,
"gene_list_for": [],
"href": "/configuration-files/IGVFFI2982KSVM/@@download/IGVFFI2982KSVM.yaml.gz",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"loci_list_for": [],
"md5sum": "7534912547203a598c4f11fe5e1ebe1c",
"release_timestamp": "2024-07-10T19:53:49.839150+00:00",
"s3_uri": "s3://igvf-files/2024/06/20/75badb6c-c57f-4f0f-af2e-1ba0e7ca9c5e/IGVFFI2982KSVM.yaml.gz",
"schema_version": "7",
"seqspec_of": [
"/sequence-files/IGVFFI3461WBDK/",
"/sequence-files/IGVFFI9043ACMD/",
"/sequence-files/IGVFFI4839QVTC/"
],
"status": "released",
"submitted_by": {
"@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
"title": "Benjamin Doughty"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin6hrs-Rep2-S4.rna.yaml.gz",
"summary": "seqspec of IGVFFI3461WBDK, IGVFFI9043ACMD, IGVFFI4839QVTC",
"upload_status": "validated",
"uuid": "75badb6c-c57f-4f0f-af2e-1ba0e7ca9c5e"
}