{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7933SDSN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7933SDSN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS7933SDSN](/measurement-sets/IGVFDS7933SDSN/) has in progress subobject auxiliary set [IGVFDS0749BSSQ](/auxiliary-sets/IGVFDS0749BSSQ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7933SDSN/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3035HZXX](/in-vitro-systems/IGVFSM3035HZXX/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM3035HZXX/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7933SDSN](/measurement-sets/IGVFDS7933SDSN/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS7933SDSN/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0749BSSQ](/auxiliary-sets/IGVFDS0749BSSQ/) has sequence file(s): [IGVFFI3508QZQO](/sequence-files/IGVFFI3508QZQO/), [IGVFFI3845WRSC](/sequence-files/IGVFFI3845WRSC/), [IGVFFI9492OGSA](/sequence-files/IGVFFI9492OGSA/), [IGVFFI9894IYQV](/sequence-files/IGVFFI9894IYQV/), [IGVFFI5991FMCF](/sequence-files/IGVFFI5991FMCF/), [IGVFFI3737JJGF](/sequence-files/IGVFFI3737JJGF/), [IGVFFI9280LARL](/sequence-files/IGVFFI9280LARL/), [IGVFFI2967UUCI](/sequence-files/IGVFFI2967UUCI/), [IGVFFI7159NXVI](/sequence-files/IGVFFI7159NXVI/), [IGVFFI9157RMLD](/sequence-files/IGVFFI9157RMLD/), [IGVFFI4731PKPW](/sequence-files/IGVFFI4731PKPW/), [IGVFFI8228JKPA](/sequence-files/IGVFFI8228JKPA/), [IGVFFI1301NZEM](/sequence-files/IGVFFI1301NZEM/), [IGVFFI4866GHCG](/sequence-files/IGVFFI4866GHCG/), [IGVFFI7348VBDI](/sequence-files/IGVFFI7348VBDI/), [IGVFFI1779XXYO](/sequence-files/IGVFFI1779XXYO/), [IGVFFI6534GIAR](/sequence-files/IGVFFI6534GIAR/), [IGVFFI2068IWLE](/sequence-files/IGVFFI2068IWLE/), [IGVFFI0088MAAD](/sequence-files/IGVFFI0088MAAD/), [IGVFFI0182DYGL](/sequence-files/IGVFFI0182DYGL/), [IGVFFI3789JGZM](/sequence-files/IGVFFI3789JGZM/), [IGVFFI7471NLRD](/sequence-files/IGVFFI7471NLRD/), [IGVFFI8524JTCM](/sequence-files/IGVFFI8524JTCM/), [IGVFFI6589AVJA](/sequence-files/IGVFFI6589AVJA/), [IGVFFI7856MTUN](/sequence-files/IGVFFI7856MTUN/), [IGVFFI6241UDKW](/sequence-files/IGVFFI6241UDKW/), [IGVFFI9695WNIE](/sequence-files/IGVFFI9695WNIE/), [IGVFFI3496OLIA](/sequence-files/IGVFFI3496OLIA/), [IGVFFI0993BCAJ](/sequence-files/IGVFFI0993BCAJ/), [IGVFFI9064TVQM](/sequence-files/IGVFFI9064TVQM/), [IGVFFI8266OKSW](/sequence-files/IGVFFI8266OKSW/), [IGVFFI8848BMJG](/sequence-files/IGVFFI8848BMJG/), [IGVFFI3382PKLE](/sequence-files/IGVFFI3382PKLE/), [IGVFFI6790WFYI](/sequence-files/IGVFFI6790WFYI/), [IGVFFI7889KYOP](/sequence-files/IGVFFI7889KYOP/), [IGVFFI7822RMOA](/sequence-files/IGVFFI7822RMOA/), [IGVFFI2614HUWS](/sequence-files/IGVFFI2614HUWS/), [IGVFFI1457JCQH](/sequence-files/IGVFFI1457JCQH/), [IGVFFI0349SQOT](/sequence-files/IGVFFI0349SQOT/), [IGVFFI3977QBRI](/sequence-files/IGVFFI3977QBRI/), [IGVFFI4225AIUG](/sequence-files/IGVFFI4225AIUG/), [IGVFFI5542JBYK](/sequence-files/IGVFFI5542JBYK/), [IGVFFI0424MXOX](/sequence-files/IGVFFI0424MXOX/), [IGVFFI4426BINF](/sequence-files/IGVFFI4426BINF/), [IGVFFI1494DYOX](/sequence-files/IGVFFI1494DYOX/), [IGVFFI3195JFDX](/sequence-files/IGVFFI3195JFDX/), [IGVFFI2764CXQB](/sequence-files/IGVFFI2764CXQB/), [IGVFFI7267OFJX](/sequence-files/IGVFFI7267OFJX/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS0749BSSQ/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0749BSSQ](/auxiliary-sets/IGVFDS0749BSSQ/) has sequence file(s) [IGVFFI3508QZQO](/sequence-files/IGVFFI3508QZQO/), [IGVFFI3845WRSC](/sequence-files/IGVFFI3845WRSC/), [IGVFFI9492OGSA](/sequence-files/IGVFFI9492OGSA/), [IGVFFI9894IYQV](/sequence-files/IGVFFI9894IYQV/), [IGVFFI5991FMCF](/sequence-files/IGVFFI5991FMCF/), [IGVFFI3737JJGF](/sequence-files/IGVFFI3737JJGF/), [IGVFFI9280LARL](/sequence-files/IGVFFI9280LARL/), [IGVFFI2967UUCI](/sequence-files/IGVFFI2967UUCI/), [IGVFFI7159NXVI](/sequence-files/IGVFFI7159NXVI/), [IGVFFI9157RMLD](/sequence-files/IGVFFI9157RMLD/), [IGVFFI4731PKPW](/sequence-files/IGVFFI4731PKPW/), [IGVFFI8228JKPA](/sequence-files/IGVFFI8228JKPA/), [IGVFFI1301NZEM](/sequence-files/IGVFFI1301NZEM/), [IGVFFI4866GHCG](/sequence-files/IGVFFI4866GHCG/), [IGVFFI7348VBDI](/sequence-files/IGVFFI7348VBDI/), [IGVFFI1779XXYO](/sequence-files/IGVFFI1779XXYO/), [IGVFFI6534GIAR](/sequence-files/IGVFFI6534GIAR/), [IGVFFI2068IWLE](/sequence-files/IGVFFI2068IWLE/), [IGVFFI0088MAAD](/sequence-files/IGVFFI0088MAAD/), [IGVFFI0182DYGL](/sequence-files/IGVFFI0182DYGL/), [IGVFFI3789JGZM](/sequence-files/IGVFFI3789JGZM/), [IGVFFI7471NLRD](/sequence-files/IGVFFI7471NLRD/), [IGVFFI8524JTCM](/sequence-files/IGVFFI8524JTCM/), [IGVFFI6589AVJA](/sequence-files/IGVFFI6589AVJA/), [IGVFFI7856MTUN](/sequence-files/IGVFFI7856MTUN/), [IGVFFI6241UDKW](/sequence-files/IGVFFI6241UDKW/), [IGVFFI9695WNIE](/sequence-files/IGVFFI9695WNIE/), [IGVFFI3496OLIA](/sequence-files/IGVFFI3496OLIA/), [IGVFFI0993BCAJ](/sequence-files/IGVFFI0993BCAJ/), [IGVFFI9064TVQM](/sequence-files/IGVFFI9064TVQM/), [IGVFFI8266OKSW](/sequence-files/IGVFFI8266OKSW/), [IGVFFI8848BMJG](/sequence-files/IGVFFI8848BMJG/), [IGVFFI3382PKLE](/sequence-files/IGVFFI3382PKLE/), [IGVFFI6790WFYI](/sequence-files/IGVFFI6790WFYI/), [IGVFFI7889KYOP](/sequence-files/IGVFFI7889KYOP/), [IGVFFI7822RMOA](/sequence-files/IGVFFI7822RMOA/), [IGVFFI2614HUWS](/sequence-files/IGVFFI2614HUWS/), [IGVFFI1457JCQH](/sequence-files/IGVFFI1457JCQH/), [IGVFFI0349SQOT](/sequence-files/IGVFFI0349SQOT/), [IGVFFI3977QBRI](/sequence-files/IGVFFI3977QBRI/), [IGVFFI4225AIUG](/sequence-files/IGVFFI4225AIUG/), [IGVFFI5542JBYK](/sequence-files/IGVFFI5542JBYK/), [IGVFFI0424MXOX](/sequence-files/IGVFFI0424MXOX/), [IGVFFI4426BINF](/sequence-files/IGVFFI4426BINF/), [IGVFFI1494DYOX](/sequence-files/IGVFFI1494DYOX/), [IGVFFI3195JFDX](/sequence-files/IGVFFI3195JFDX/), [IGVFFI2764CXQB](/sequence-files/IGVFFI2764CXQB/), [IGVFFI7267OFJX](/sequence-files/IGVFFI7267OFJX/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0749BSSQ/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0749BSSQ](/auxiliary-sets/IGVFDS0749BSSQ/) 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/IGVFDS0749BSSQ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0749BSSQ/",
"accession": "IGVFDS0749BSSQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing"
}
],
"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_file_sets": [
{
"@id": "/measurement-sets/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:04.619473+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS5031MNRR/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:05:33.167541+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3035HZXX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3035HZXX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 26-50% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T20:54:07.586704+00:00",
"summary": "Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "9f757a98-04d1-4835-9b18-192c1cd727cd"
}