{
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"FileSet",
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],
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"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": {
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"component": "functional characterization",
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"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
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"creation_timestamp": "2024-07-02T23:41:56.636236+00:00",
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{
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],
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}
],
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{
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"controlled_access": false,
"creation_timestamp": "2024-07-03T00:35:41.552830+00:00",
"file_format": "tsv",
"file_size": 486,
"href": "/tabular-files/IGVFFI1487CLSF/@@download/IGVFFI1487CLSF.tsv.gz",
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"status": "released",
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}
],
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],
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{
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],
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},
{
"@id": "/measurement-sets/IGVFDS3215BSOP/",
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"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR1_S41",
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],
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},
{
"@id": "/measurement-sets/IGVFDS1681VDMR/",
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"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR1_S37",
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"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR4_S139"
],
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"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0488GVJK/",
"accession": "IGVFDS0488GVJK",
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"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR1_S39",
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"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR4_S141"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5041NPBP/",
"accession": "IGVFDS5041NPBP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR1_S42",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR2_S48",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR3_S138",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR4_S144"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:28:23.119933+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1476GCQU/",
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"Sample",
"Item"
],
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"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR2_S43",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR3_S133",
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],
"classifications": [
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],
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],
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{
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"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
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"status": "released"
}
],
"sample_terms": [
{
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"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"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/",
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"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
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"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR1_S38",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR2_S44",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR3_S134",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR4_S140"
],
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],
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],
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{
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"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
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}
],
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{
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"Item"
],
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],
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"summary": "HCT116",
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}
],
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"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM2659OCKX/",
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"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2659OCKX",
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"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR2_S45",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR3_S135",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR4_S141"
],
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],
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],
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{
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"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
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"status": "released"
}
],
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{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
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"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/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1961BHPA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR1_S40",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR2_S46",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR3_S136",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR4_S142"
],
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],
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],
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{
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"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
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"status": "released"
}
],
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{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
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"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM3377SBLH/",
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"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
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"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR3_S137",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinE-PCR4_S143"
],
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],
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],
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{
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"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released"
}
],
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{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"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/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
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"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR1_S42",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR2_S48",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR3_S138",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR4_S144"
],
"classifications": [
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],
"construct_library_sets": [
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],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"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"
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
"title": "Benjamin Doughty"
},
"submitted_files_timestamp": "2024-07-03T00:35:41.552830+00:00",
"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",
"uuid": "796a8e00-0663-49d8-8db8-3e2192f90566"
}