{
"@context": "/terms/",
"@id": "/sequence-files/IGVFFI0163GSPS/",
"@type": [
"SequenceFile",
"File",
"Item"
],
"accession": "IGVFFI0163GSPS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinE-PCR3-Rep1_S203"
],
"assay_titles": [
"CRISPR FlowFISH screen"
],
"audit": {},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"content_md5sum": "3cc136b51f137fc6fe40543b3e149f03",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:55:21.746354+00:00",
"externally_hosted": false,
"file_format": "fastq",
"file_set": {
"@id": "/auxiliary-sets/IGVFDS2217TMIN/",
"accession": "IGVFDS2217TMIN",
"file_set_type": "gRNA sequencing",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2128WJNF/",
"accession": "IGVFSM2128WJNF",
"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 E for 80-90% expression of FAM3C) 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 many genomic loci"
},
"file_size": 24852380,
"gene_list_for": [],
"href": "/sequence-files/IGVFFI0163GSPS/@@download/IGVFFI0163GSPS.fastq.gz",
"index": "AATGTTCT:ATTG",
"input_file_for": [
"/tabular-files/IGVFFI8715FPDT/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"loci_list_for": [],
"maximum_read_length": 21,
"md5sum": "fa8b0599005c4dc2788a728ed25c9bdd",
"mean_read_length": 21,
"minimum_read_length": 21,
"read_count": 1152126,
"release_timestamp": "2024-07-10T20:13:18.495082+00:00",
"s3_uri": "s3://igvf-files/2024/06/01/21422fd4-58fa-419d-9b1c-e7c9a4c211d5/IGVFFI0163GSPS.fastq.gz",
"schema_version": "14",
"seqspecs": [
"/configuration-files/IGVFFI0980GKKZ/"
],
"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/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF2-BinE-PCR3-Rep1_S203_R1_001.fastq.gz",
"summary": "reads from sequencing run 1",
"upload_status": "validated",
"uuid": "21422fd4-58fa-419d-9b1c-e7c9a4c211d5"
}