{
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],
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],
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{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI5182VLZN](/tabular-files/IGVFFI5182VLZN/) 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/IGVFFI5182VLZN/"
}
]
},
"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": "2024-07-02T23:41:55.907478+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": "2024-07-03T00:35:37.219464+00:00",
"file_format": "tsv",
"file_size": 478,
"href": "/tabular-files/IGVFFI5182VLZN/@@download/IGVFFI5182VLZN.tsv.gz",
"s3_uri": "s3://igvf-files/2024/07/03/840aa062-20de-423e-9c18-57d5e1be58f9/IGVFFI5182VLZN.tsv.gz",
"status": "released",
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}
],
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],
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"title": "Jesse Engreitz, Stanford"
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},
{
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],
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"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4623YYCA/",
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"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR1_S18",
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"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR4_S120"
],
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},
{
"@id": "/measurement-sets/IGVFDS4649YECB/",
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"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR1_S13",
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"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S109"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8133FFMV/",
"accession": "IGVFDS8133FFMV",
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"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR1_S17",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR2_S23",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9308CBBI/",
"accession": "IGVFDS9308CBBI",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:28:09.693562+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8346JZPG/",
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"Biosample",
"Sample",
"Item"
],
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"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR1_S13",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR2_S19",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR4_S115",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR3_S109"
],
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],
"construct_library_sets": [
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"modifications": [
{
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"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"
],
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"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/IGVFSM3263KXLP/",
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"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3263KXLP",
"aliases": [
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"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR2_S20",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S110",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR4_S116"
],
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],
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"/construct-library-sets/IGVFDS7846UISG/"
],
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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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{
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"OntologyTerm",
"Item"
],
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"igvf:HCT116"
],
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"summary": "HCT116",
"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/IGVFSM7071BULA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7071BULA",
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"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117"
],
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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"
}
],
"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 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/IGVFSM0606BETP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0606BETP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR1_S16",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR2_S22",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR3_S112",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinD-PCR4_S118"
],
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],
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],
"modifications": [
{
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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 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/IGVFSM9074NPMT/",
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"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
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"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
],
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"cell line"
],
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"/construct-library-sets/IGVFDS7846UISG/"
],
"modifications": [
{
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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/IGVFSM1737WNTH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1737WNTH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR1_S18",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR2_S24",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR3_S114",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinF-PCR4_S120"
],
"classifications": [
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],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"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": "2024-07-03T00:35:37.219464+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": "5180de3d-629a-453d-9378-fd66c1f4c670"
}