{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0595OBOA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0595OBOA",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep4-BinA_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 [IGVFDS0595OBOA](/measurement-sets/IGVFDS0595OBOA/) has in progress subobject auxiliary set [IGVFDS4409XWPC](/auxiliary-sets/IGVFDS4409XWPC/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0595OBOA/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4893GPVV](/in-vitro-systems/IGVFSM4893GPVV/) 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/IGVFSM4893GPVV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0595OBOA](/measurement-sets/IGVFDS0595OBOA/) 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/IGVFDS0595OBOA/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4409XWPC](/auxiliary-sets/IGVFDS4409XWPC/) has sequence file(s): [IGVFFI1562DSMD](/sequence-files/IGVFFI1562DSMD/), [IGVFFI8952ZDMH](/sequence-files/IGVFFI8952ZDMH/), [IGVFFI0116FTMZ](/sequence-files/IGVFFI0116FTMZ/), [IGVFFI5932ENNC](/sequence-files/IGVFFI5932ENNC/), [IGVFFI2195KDOM](/sequence-files/IGVFFI2195KDOM/), [IGVFFI9706ZNBC](/sequence-files/IGVFFI9706ZNBC/), [IGVFFI5316QIUX](/sequence-files/IGVFFI5316QIUX/), [IGVFFI7859JTGD](/sequence-files/IGVFFI7859JTGD/), [IGVFFI2811QOMX](/sequence-files/IGVFFI2811QOMX/), [IGVFFI1186MENK](/sequence-files/IGVFFI1186MENK/), [IGVFFI6281HWPB](/sequence-files/IGVFFI6281HWPB/), [IGVFFI8898DYAB](/sequence-files/IGVFFI8898DYAB/), [IGVFFI0299PRHE](/sequence-files/IGVFFI0299PRHE/), [IGVFFI5139YEUZ](/sequence-files/IGVFFI5139YEUZ/), [IGVFFI8074JBCF](/sequence-files/IGVFFI8074JBCF/), [IGVFFI9175PZYF](/sequence-files/IGVFFI9175PZYF/), [IGVFFI2303GWMJ](/sequence-files/IGVFFI2303GWMJ/), [IGVFFI2465UXYE](/sequence-files/IGVFFI2465UXYE/), [IGVFFI8067ILTA](/sequence-files/IGVFFI8067ILTA/), [IGVFFI3897LUSJ](/sequence-files/IGVFFI3897LUSJ/), [IGVFFI8504HKOE](/sequence-files/IGVFFI8504HKOE/), [IGVFFI9402WGFC](/sequence-files/IGVFFI9402WGFC/), [IGVFFI3515VQWV](/sequence-files/IGVFFI3515VQWV/), [IGVFFI2341QUEX](/sequence-files/IGVFFI2341QUEX/), [IGVFFI5248HHSM](/sequence-files/IGVFFI5248HHSM/), [IGVFFI0201HMLK](/sequence-files/IGVFFI0201HMLK/), [IGVFFI0470AMOB](/sequence-files/IGVFFI0470AMOB/), [IGVFFI8202YCKI](/sequence-files/IGVFFI8202YCKI/), [IGVFFI1579LBGJ](/sequence-files/IGVFFI1579LBGJ/), [IGVFFI9173DQSG](/sequence-files/IGVFFI9173DQSG/), [IGVFFI6214RUQQ](/sequence-files/IGVFFI6214RUQQ/), [IGVFFI2180YRNU](/sequence-files/IGVFFI2180YRNU/), [IGVFFI8972TMMD](/sequence-files/IGVFFI8972TMMD/), [IGVFFI6409LIKI](/sequence-files/IGVFFI6409LIKI/), [IGVFFI4551NIEK](/sequence-files/IGVFFI4551NIEK/), [IGVFFI1490XWNF](/sequence-files/IGVFFI1490XWNF/), [IGVFFI4285PDQM](/sequence-files/IGVFFI4285PDQM/), [IGVFFI7893OAAA](/sequence-files/IGVFFI7893OAAA/), [IGVFFI7296ABQX](/sequence-files/IGVFFI7296ABQX/), [IGVFFI9572VVCE](/sequence-files/IGVFFI9572VVCE/), [IGVFFI6877PUCW](/sequence-files/IGVFFI6877PUCW/), [IGVFFI0271OWCU](/sequence-files/IGVFFI0271OWCU/), [IGVFFI2533RTEK](/sequence-files/IGVFFI2533RTEK/), [IGVFFI8315JDIR](/sequence-files/IGVFFI8315JDIR/), [IGVFFI3737WUMM](/sequence-files/IGVFFI3737WUMM/), [IGVFFI2446OVLW](/sequence-files/IGVFFI2446OVLW/), [IGVFFI0755EFIB](/sequence-files/IGVFFI0755EFIB/), [IGVFFI5709UQBE](/sequence-files/IGVFFI5709UQBE/) 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/IGVFDS4409XWPC/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4409XWPC](/auxiliary-sets/IGVFDS4409XWPC/) has sequence file(s) [IGVFFI1562DSMD](/sequence-files/IGVFFI1562DSMD/), [IGVFFI8952ZDMH](/sequence-files/IGVFFI8952ZDMH/), [IGVFFI0116FTMZ](/sequence-files/IGVFFI0116FTMZ/), [IGVFFI5932ENNC](/sequence-files/IGVFFI5932ENNC/), [IGVFFI2195KDOM](/sequence-files/IGVFFI2195KDOM/), [IGVFFI9706ZNBC](/sequence-files/IGVFFI9706ZNBC/), [IGVFFI5316QIUX](/sequence-files/IGVFFI5316QIUX/), [IGVFFI7859JTGD](/sequence-files/IGVFFI7859JTGD/), [IGVFFI2811QOMX](/sequence-files/IGVFFI2811QOMX/), [IGVFFI1186MENK](/sequence-files/IGVFFI1186MENK/), [IGVFFI6281HWPB](/sequence-files/IGVFFI6281HWPB/), [IGVFFI8898DYAB](/sequence-files/IGVFFI8898DYAB/), [IGVFFI0299PRHE](/sequence-files/IGVFFI0299PRHE/), [IGVFFI5139YEUZ](/sequence-files/IGVFFI5139YEUZ/), [IGVFFI8074JBCF](/sequence-files/IGVFFI8074JBCF/), [IGVFFI9175PZYF](/sequence-files/IGVFFI9175PZYF/), [IGVFFI2303GWMJ](/sequence-files/IGVFFI2303GWMJ/), [IGVFFI2465UXYE](/sequence-files/IGVFFI2465UXYE/), [IGVFFI8067ILTA](/sequence-files/IGVFFI8067ILTA/), [IGVFFI3897LUSJ](/sequence-files/IGVFFI3897LUSJ/), [IGVFFI8504HKOE](/sequence-files/IGVFFI8504HKOE/), [IGVFFI9402WGFC](/sequence-files/IGVFFI9402WGFC/), [IGVFFI3515VQWV](/sequence-files/IGVFFI3515VQWV/), [IGVFFI2341QUEX](/sequence-files/IGVFFI2341QUEX/), [IGVFFI5248HHSM](/sequence-files/IGVFFI5248HHSM/), [IGVFFI0201HMLK](/sequence-files/IGVFFI0201HMLK/), [IGVFFI0470AMOB](/sequence-files/IGVFFI0470AMOB/), [IGVFFI8202YCKI](/sequence-files/IGVFFI8202YCKI/), [IGVFFI1579LBGJ](/sequence-files/IGVFFI1579LBGJ/), [IGVFFI9173DQSG](/sequence-files/IGVFFI9173DQSG/), [IGVFFI6214RUQQ](/sequence-files/IGVFFI6214RUQQ/), [IGVFFI2180YRNU](/sequence-files/IGVFFI2180YRNU/), [IGVFFI8972TMMD](/sequence-files/IGVFFI8972TMMD/), [IGVFFI6409LIKI](/sequence-files/IGVFFI6409LIKI/), [IGVFFI4551NIEK](/sequence-files/IGVFFI4551NIEK/), [IGVFFI1490XWNF](/sequence-files/IGVFFI1490XWNF/), [IGVFFI4285PDQM](/sequence-files/IGVFFI4285PDQM/), [IGVFFI7893OAAA](/sequence-files/IGVFFI7893OAAA/), [IGVFFI7296ABQX](/sequence-files/IGVFFI7296ABQX/), [IGVFFI9572VVCE](/sequence-files/IGVFFI9572VVCE/), [IGVFFI6877PUCW](/sequence-files/IGVFFI6877PUCW/), [IGVFFI0271OWCU](/sequence-files/IGVFFI0271OWCU/), [IGVFFI2533RTEK](/sequence-files/IGVFFI2533RTEK/), [IGVFFI8315JDIR](/sequence-files/IGVFFI8315JDIR/), [IGVFFI3737WUMM](/sequence-files/IGVFFI3737WUMM/), [IGVFFI2446OVLW](/sequence-files/IGVFFI2446OVLW/), [IGVFFI0755EFIB](/sequence-files/IGVFFI0755EFIB/), [IGVFFI5709UQBE](/sequence-files/IGVFFI5709UQBE/) 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/IGVFDS4409XWPC/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4409XWPC](/auxiliary-sets/IGVFDS4409XWPC/) 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/IGVFDS4409XWPC/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4409XWPC/",
"accession": "IGVFDS4409XWPC",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep4-BinA_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": "2023-12-13T08:48:08.053217+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": "2023-12-20T23:08:39.221643+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4893GPVV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4893GPVV",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep4-BinA"
],
"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 0-25% 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": "2023-12-13T09:52:29.009771+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": "9294f0be-c60c-45ef-b177-3b9616138751"
}