{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
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],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI1231XMQS](/tabular-files/IGVFFI1231XMQS/) 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/IGVFFI1231XMQS/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1546MEZJ](/auxiliary-sets/IGVFDS1546MEZJ/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS1546MEZJ/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-07-02T23:42:00.710814+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell sorting",
"files": [
{
"@id": "/tabular-files/IGVFFI1231XMQS/",
"accession": "IGVFFI1231XMQS",
"aliases": [
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],
"content_type": "sample sort parameters",
"creation_timestamp": "2024-07-03T00:36:01.266979+00:00",
"file_format": "tsv",
"file_size": 457,
"href": "/tabular-files/IGVFFI1231XMQS/@@download/IGVFFI1231XMQS.tsv.gz",
"s3_uri": "s3://igvf-files/2024/07/03/03cc88ea-4b48-46fc-9cd7-3b49712409ce/IGVFFI1231XMQS.tsv.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/sortparams/220307B014_2.ssfa2.tsv.gz",
"upload_status": "validated"
}
],
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"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
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{
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"accession": "IGVFDS1338GOGT",
"aliases": [
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"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
},
{
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"accession": "IGVFDS7398YKXX",
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"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR2-Rep1_S7",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR3-Rep1_S55",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR4-Rep1_S61"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
},
{
"@id": "/measurement-sets/IGVFDS2697OVVG/",
"accession": "IGVFDS2697OVVG",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR1-Rep1_S2",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR2-Rep1_S8",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR3-Rep1_S56",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR4-Rep1_S62"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
},
{
"@id": "/measurement-sets/IGVFDS0674KOZU/",
"accession": "IGVFDS0674KOZU",
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"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
},
{
"@id": "/measurement-sets/IGVFDS0884TWTU/",
"accession": "IGVFDS0884TWTU",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR1-Rep1_S5",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR3-Rep1_S59",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
},
{
"@id": "/measurement-sets/IGVFDS9212JUFJ/",
"accession": "IGVFDS9212JUFJ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR1-Rep1_S3",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR2-Rep1_S9",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR3-Rep1_S57",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR4-Rep1_S63"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:29:45.820672+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7231THBU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7231THBU",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR1-Rep1_S1",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR2-Rep1_S7",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR3-Rep1_S55",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR4-Rep1_S61"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"modifications": [
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"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 A for 0-10% expression of SSFA2) modified with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM0430YSKQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0430YSKQ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR1-Rep1_S2",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR2-Rep1_S8",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR3-Rep1_S56",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR4-Rep1_S62"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"modifications": [
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"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 B for 10-20% expression of SSFA2) modified with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM7889BDAF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7889BDAF",
"aliases": [
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"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR2-Rep1_S9",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR3-Rep1_S57",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinC-PCR4-Rep1_S63"
],
"classifications": [
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],
"construct_library_sets": [
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],
"modifications": [
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"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 SSFA2) modified with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM5613UEVU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5613UEVU",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"classifications": [
"cell line"
],
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],
"modifications": [
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],
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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 SSFA2) modified with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM7435FSSP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7435FSSP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR1-Rep1_S5",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR3-Rep1_S59",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65"
],
"classifications": [
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],
"construct_library_sets": [
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],
"modifications": [
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"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 E for 80-90% expression of SSFA2) modified with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM4326ZGNE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4326ZGNE",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
],
"classifications": [
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],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"modifications": [
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"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 SSFA2) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
"title": "Benjamin Doughty"
},
"submitted_files_timestamp": "2024-07-03T00:36:01.266979+00:00",
"summary": "cell sorting for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, ... and 4 more measurement sets",
"uuid": "b246b1ed-a85d-42c0-a021-185556ff1075"
}