{
"@context": "/terms/",
"@id": "/sequence-files/IGVFFI2191UDNG/",
"@type": [
"SequenceFile",
"File",
"Item"
],
"accession": "IGVFFI2191UDNG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99"
],
"assay_titles": [
"CRISPR FlowFISH screen"
],
"audit": {},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"content_md5sum": "d43e439ed4da01bb59037ff2cd4cbb65",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:00.480408+00:00",
"externally_hosted": false,
"file_format": "fastq",
"file_set": {
"@id": "/auxiliary-sets/IGVFDS5389PFCH/",
"accession": "IGVFDS5389PFCH",
"file_set_type": "gRNA sequencing",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6480FETB/",
"accession": "IGVFSM6480FETB",
"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 (sorting details: FACS bin C for 35-45% expression of CCND1) 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": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci"
},
"file_size": 7816883,
"gene_list_for": [],
"href": "/sequence-files/IGVFFI2191UDNG/@@download/IGVFFI2191UDNG.fastq.gz",
"index": "GCACATCT:CATA",
"input_file_for": [
"/tabular-files/IGVFFI3634OXIQ/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"loci_list_for": [],
"maximum_read_length": 21,
"md5sum": "c7095abe1850403125a7d18a29bb915b",
"mean_read_length": 21,
"minimum_read_length": 21,
"read_count": 333086,
"release_timestamp": "2024-07-10T20:23:13.643435+00:00",
"s3_uri": "s3://igvf-files/2024/06/01/6e1958c6-580f-4ff0-9fca-849d53cce21d/IGVFFI2191UDNG.fastq.gz",
"schema_version": "14",
"seqspecs": [
"/configuration-files/IGVFFI2434JICM/"
],
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"sequencing_run": 1,
"status": "released",
"submitted_by": {
"@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
"title": "Benjamin Doughty"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinC-PCR2_S99_R1_001.fastq.gz",
"summary": "reads from sequencing run 1",
"upload_status": "validated",
"uuid": "6e1958c6-580f-4ff0-9fca-849d53cce21d"
}