{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8782KHRJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8782KHRJ",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-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 [IGVFDS8782KHRJ](/measurement-sets/IGVFDS8782KHRJ/) has in progress subobject auxiliary set [IGVFDS4967IZZB](/auxiliary-sets/IGVFDS4967IZZB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8782KHRJ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2181BEKF](/in-vitro-systems/IGVFSM2181BEKF/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM2181BEKF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8782KHRJ](/measurement-sets/IGVFDS8782KHRJ/) 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/IGVFDS8782KHRJ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4967IZZB](/auxiliary-sets/IGVFDS4967IZZB/) has sequence file(s): [IGVFFI4263IVOQ](/sequence-files/IGVFFI4263IVOQ/), [IGVFFI9141IFTT](/sequence-files/IGVFFI9141IFTT/), [IGVFFI7559USND](/sequence-files/IGVFFI7559USND/), [IGVFFI7729UUFF](/sequence-files/IGVFFI7729UUFF/), [IGVFFI3008JMEQ](/sequence-files/IGVFFI3008JMEQ/), [IGVFFI4273LOIP](/sequence-files/IGVFFI4273LOIP/), [IGVFFI1428DKAX](/sequence-files/IGVFFI1428DKAX/), [IGVFFI7898BHEJ](/sequence-files/IGVFFI7898BHEJ/), [IGVFFI3245GGFN](/sequence-files/IGVFFI3245GGFN/), [IGVFFI7622RETL](/sequence-files/IGVFFI7622RETL/), [IGVFFI4070WLOA](/sequence-files/IGVFFI4070WLOA/), [IGVFFI0767OCUM](/sequence-files/IGVFFI0767OCUM/), [IGVFFI9517XYGY](/sequence-files/IGVFFI9517XYGY/), [IGVFFI5194LQTT](/sequence-files/IGVFFI5194LQTT/), [IGVFFI4368VHVO](/sequence-files/IGVFFI4368VHVO/), [IGVFFI5947WRYM](/sequence-files/IGVFFI5947WRYM/), [IGVFFI2320YWUN](/sequence-files/IGVFFI2320YWUN/), [IGVFFI5829KRCX](/sequence-files/IGVFFI5829KRCX/), [IGVFFI3583LXZN](/sequence-files/IGVFFI3583LXZN/), [IGVFFI0810JDHU](/sequence-files/IGVFFI0810JDHU/), [IGVFFI1236ETZW](/sequence-files/IGVFFI1236ETZW/), [IGVFFI9576JIGE](/sequence-files/IGVFFI9576JIGE/), [IGVFFI8707JMVM](/sequence-files/IGVFFI8707JMVM/), [IGVFFI3579XEQR](/sequence-files/IGVFFI3579XEQR/), [IGVFFI4799JDBO](/sequence-files/IGVFFI4799JDBO/), [IGVFFI2840IDLR](/sequence-files/IGVFFI2840IDLR/), [IGVFFI3343IOCF](/sequence-files/IGVFFI3343IOCF/), [IGVFFI0564ZSPY](/sequence-files/IGVFFI0564ZSPY/), [IGVFFI0251RLLU](/sequence-files/IGVFFI0251RLLU/), [IGVFFI5545JZBQ](/sequence-files/IGVFFI5545JZBQ/), [IGVFFI1267TXVN](/sequence-files/IGVFFI1267TXVN/), [IGVFFI0920TLXK](/sequence-files/IGVFFI0920TLXK/), [IGVFFI2080KORO](/sequence-files/IGVFFI2080KORO/), [IGVFFI2045QXGB](/sequence-files/IGVFFI2045QXGB/), [IGVFFI8632GQZJ](/sequence-files/IGVFFI8632GQZJ/), [IGVFFI8857XOGP](/sequence-files/IGVFFI8857XOGP/), [IGVFFI3133YOXP](/sequence-files/IGVFFI3133YOXP/), [IGVFFI3676ZFWX](/sequence-files/IGVFFI3676ZFWX/), [IGVFFI6173XWJJ](/sequence-files/IGVFFI6173XWJJ/), [IGVFFI9144MQFL](/sequence-files/IGVFFI9144MQFL/), [IGVFFI5368AJWA](/sequence-files/IGVFFI5368AJWA/), [IGVFFI6852DZEU](/sequence-files/IGVFFI6852DZEU/), [IGVFFI5532SCGV](/sequence-files/IGVFFI5532SCGV/), [IGVFFI0233NMTO](/sequence-files/IGVFFI0233NMTO/), [IGVFFI8277MANK](/sequence-files/IGVFFI8277MANK/), [IGVFFI7748RUUE](/sequence-files/IGVFFI7748RUUE/), [IGVFFI2266OLMK](/sequence-files/IGVFFI2266OLMK/), [IGVFFI0927MEVY](/sequence-files/IGVFFI0927MEVY/) 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/IGVFDS4967IZZB/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4967IZZB](/auxiliary-sets/IGVFDS4967IZZB/) has sequence file(s) [IGVFFI4263IVOQ](/sequence-files/IGVFFI4263IVOQ/), [IGVFFI9141IFTT](/sequence-files/IGVFFI9141IFTT/), [IGVFFI7559USND](/sequence-files/IGVFFI7559USND/), [IGVFFI7729UUFF](/sequence-files/IGVFFI7729UUFF/), [IGVFFI3008JMEQ](/sequence-files/IGVFFI3008JMEQ/), [IGVFFI4273LOIP](/sequence-files/IGVFFI4273LOIP/), [IGVFFI1428DKAX](/sequence-files/IGVFFI1428DKAX/), [IGVFFI7898BHEJ](/sequence-files/IGVFFI7898BHEJ/), [IGVFFI3245GGFN](/sequence-files/IGVFFI3245GGFN/), [IGVFFI7622RETL](/sequence-files/IGVFFI7622RETL/), [IGVFFI4070WLOA](/sequence-files/IGVFFI4070WLOA/), [IGVFFI0767OCUM](/sequence-files/IGVFFI0767OCUM/), [IGVFFI9517XYGY](/sequence-files/IGVFFI9517XYGY/), [IGVFFI5194LQTT](/sequence-files/IGVFFI5194LQTT/), [IGVFFI4368VHVO](/sequence-files/IGVFFI4368VHVO/), [IGVFFI5947WRYM](/sequence-files/IGVFFI5947WRYM/), [IGVFFI2320YWUN](/sequence-files/IGVFFI2320YWUN/), [IGVFFI5829KRCX](/sequence-files/IGVFFI5829KRCX/), [IGVFFI3583LXZN](/sequence-files/IGVFFI3583LXZN/), [IGVFFI0810JDHU](/sequence-files/IGVFFI0810JDHU/), [IGVFFI1236ETZW](/sequence-files/IGVFFI1236ETZW/), [IGVFFI9576JIGE](/sequence-files/IGVFFI9576JIGE/), [IGVFFI8707JMVM](/sequence-files/IGVFFI8707JMVM/), [IGVFFI3579XEQR](/sequence-files/IGVFFI3579XEQR/), [IGVFFI4799JDBO](/sequence-files/IGVFFI4799JDBO/), [IGVFFI2840IDLR](/sequence-files/IGVFFI2840IDLR/), [IGVFFI3343IOCF](/sequence-files/IGVFFI3343IOCF/), [IGVFFI0564ZSPY](/sequence-files/IGVFFI0564ZSPY/), [IGVFFI0251RLLU](/sequence-files/IGVFFI0251RLLU/), [IGVFFI5545JZBQ](/sequence-files/IGVFFI5545JZBQ/), [IGVFFI1267TXVN](/sequence-files/IGVFFI1267TXVN/), [IGVFFI0920TLXK](/sequence-files/IGVFFI0920TLXK/), [IGVFFI2080KORO](/sequence-files/IGVFFI2080KORO/), [IGVFFI2045QXGB](/sequence-files/IGVFFI2045QXGB/), [IGVFFI8632GQZJ](/sequence-files/IGVFFI8632GQZJ/), [IGVFFI8857XOGP](/sequence-files/IGVFFI8857XOGP/), [IGVFFI3133YOXP](/sequence-files/IGVFFI3133YOXP/), [IGVFFI3676ZFWX](/sequence-files/IGVFFI3676ZFWX/), [IGVFFI6173XWJJ](/sequence-files/IGVFFI6173XWJJ/), [IGVFFI9144MQFL](/sequence-files/IGVFFI9144MQFL/), [IGVFFI5368AJWA](/sequence-files/IGVFFI5368AJWA/), [IGVFFI6852DZEU](/sequence-files/IGVFFI6852DZEU/), [IGVFFI5532SCGV](/sequence-files/IGVFFI5532SCGV/), [IGVFFI0233NMTO](/sequence-files/IGVFFI0233NMTO/), [IGVFFI8277MANK](/sequence-files/IGVFFI8277MANK/), [IGVFFI7748RUUE](/sequence-files/IGVFFI7748RUUE/), [IGVFFI2266OLMK](/sequence-files/IGVFFI2266OLMK/), [IGVFFI0927MEVY](/sequence-files/IGVFFI0927MEVY/) 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/IGVFDS4967IZZB/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4967IZZB](/auxiliary-sets/IGVFDS4967IZZB/) 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/IGVFDS4967IZZB/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4967IZZB/",
"accession": "IGVFDS4967IZZB",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:48:04.835932+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS6299IJHG/"
],
"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": "2023-12-20T23:08:56.371156+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2181BEKF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2181BEKF",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-BinB"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"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_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat 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": "20",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T09:36:38.264170+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": "5930f2df-4703-431e-b641-f643117fbff4"
}