{
"@context": "/terms/",
"@id": "/tabular-files/IGVFFI1487CLSF/",
"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI1487CLSF",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_file_CRUDO_KITLG-Auxin0hrs-FF4"
],
"assay_titles": [
"CRISPR FlowFISH screen"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI1487CLSF](/tabular-files/IGVFFI1487CLSF/) has no `file_format_specifications`. Tabular files are expected to link to a file format specifications document describing the headers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_tabular_file_no_file_format_specifications",
"path": "/tabular-files/IGVFFI1487CLSF/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"barcode_map_for": [],
"content_md5sum": "642767d45b1d3d53474e6bb43259e608",
"content_type": "sample sort parameters",
"controlled_access": false,
"creation_timestamp": "2024-07-03T00:35:41.552830+00:00",
"file_format": "tsv",
"file_set": {
"@id": "/auxiliary-sets/IGVFDS4590CBRM/",
"accession": "IGVFDS4590CBRM",
"file_set_type": "cell sorting",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1476GCQU/",
"accession": "IGVFSM1476GCQU",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released",
"summary": "inactive AID system targeting RAD21"
}
],
"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 A for 0-10% expression of KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM8103DFGV/",
"accession": "IGVFSM8103DFGV",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released",
"summary": "inactive AID system targeting RAD21"
}
],
"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 B for 10-20% expression of KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM2659OCKX/",
"accession": "IGVFSM2659OCKX",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released",
"summary": "inactive AID system targeting RAD21"
}
],
"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 KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM1961BHPA/",
"accession": "IGVFSM1961BHPA",
"classifications": [
"cell line"
],
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{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released",
"summary": "inactive AID system targeting RAD21"
}
],
"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 D for 55-65% expression of KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM3377SBLH/",
"accession": "IGVFSM3377SBLH",
"classifications": [
"cell line"
],
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{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released",
"summary": "inactive AID system targeting RAD21"
}
],
"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 KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM1131LTFK/",
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"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released",
"summary": "inactive AID system targeting RAD21"
}
],
"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 F for 80-100% expression of KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"status": "released",
"summary": "cell sorting for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, ... and 4 more measurement sets"
},
"file_size": 486,
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"href": "/tabular-files/IGVFFI1487CLSF/@@download/IGVFFI1487CLSF.tsv.gz",
"input_file_for": [
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],
"integrated_in": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"loci_list_for": [],
"md5sum": "2242fe8f227f6755c98d014ec72d8a40",
"release_timestamp": "2024-07-10T20:28:23.407986+00:00",
"s3_uri": "s3://igvf-files/2024/07/03/42aa6c4b-8778-42a6-b398-a9a4cbd34867/IGVFFI1487CLSF.tsv.gz",
"schema_version": "13",
"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/sortparams2/220104B013_5.tsv.gz",
"summary": "sample sort parameters",
"upload_status": "validated",
"uuid": "42aa6c4b-8778-42a6-b398-a9a4cbd34867"
}