{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5856FZKF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5856FZKF",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-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 in vitro system [IGVFSM7961LTZR](/in-vitro-systems/IGVFSM7961LTZR/) 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/IGVFSM7961LTZR/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5856FZKF](/measurement-sets/IGVFDS5856FZKF/) has in progress subobject auxiliary set [IGVFDS3158RHSP](/auxiliary-sets/IGVFDS3158RHSP/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5856FZKF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3158RHSP](/auxiliary-sets/IGVFDS3158RHSP/) has sequence file(s): [IGVFFI1815CRNJ](/sequence-files/IGVFFI1815CRNJ/), [IGVFFI2427CLUI](/sequence-files/IGVFFI2427CLUI/), [IGVFFI6845LMPY](/sequence-files/IGVFFI6845LMPY/), [IGVFFI5018WXNV](/sequence-files/IGVFFI5018WXNV/), [IGVFFI6397SUJC](/sequence-files/IGVFFI6397SUJC/), [IGVFFI3158RNKH](/sequence-files/IGVFFI3158RNKH/), [IGVFFI1282FWJQ](/sequence-files/IGVFFI1282FWJQ/), [IGVFFI7347GBNW](/sequence-files/IGVFFI7347GBNW/), [IGVFFI7734RLWM](/sequence-files/IGVFFI7734RLWM/), [IGVFFI5742CFJG](/sequence-files/IGVFFI5742CFJG/), [IGVFFI2823RWAW](/sequence-files/IGVFFI2823RWAW/), [IGVFFI3463QFUD](/sequence-files/IGVFFI3463QFUD/), [IGVFFI4047BBPJ](/sequence-files/IGVFFI4047BBPJ/), [IGVFFI3260ODND](/sequence-files/IGVFFI3260ODND/), [IGVFFI9237NRDU](/sequence-files/IGVFFI9237NRDU/), [IGVFFI7199EJUV](/sequence-files/IGVFFI7199EJUV/), [IGVFFI6029OCBI](/sequence-files/IGVFFI6029OCBI/), [IGVFFI1070KTCG](/sequence-files/IGVFFI1070KTCG/), [IGVFFI0578DORF](/sequence-files/IGVFFI0578DORF/), [IGVFFI9545EZRY](/sequence-files/IGVFFI9545EZRY/), [IGVFFI4721AXTO](/sequence-files/IGVFFI4721AXTO/), [IGVFFI1458HQEB](/sequence-files/IGVFFI1458HQEB/), [IGVFFI1130XONB](/sequence-files/IGVFFI1130XONB/), [IGVFFI4075FCRP](/sequence-files/IGVFFI4075FCRP/), [IGVFFI7502LMVQ](/sequence-files/IGVFFI7502LMVQ/), [IGVFFI3549ITFF](/sequence-files/IGVFFI3549ITFF/), [IGVFFI2031SKIL](/sequence-files/IGVFFI2031SKIL/), [IGVFFI2351TLFO](/sequence-files/IGVFFI2351TLFO/), [IGVFFI2520CEXS](/sequence-files/IGVFFI2520CEXS/), [IGVFFI6735AEPI](/sequence-files/IGVFFI6735AEPI/), [IGVFFI6748XRYL](/sequence-files/IGVFFI6748XRYL/), [IGVFFI1560IQYJ](/sequence-files/IGVFFI1560IQYJ/), [IGVFFI4859XPET](/sequence-files/IGVFFI4859XPET/), [IGVFFI6533YLMJ](/sequence-files/IGVFFI6533YLMJ/), [IGVFFI1023NAVB](/sequence-files/IGVFFI1023NAVB/), [IGVFFI7429CIJF](/sequence-files/IGVFFI7429CIJF/), [IGVFFI7113WZPT](/sequence-files/IGVFFI7113WZPT/), [IGVFFI0683KABS](/sequence-files/IGVFFI0683KABS/), [IGVFFI5551STSB](/sequence-files/IGVFFI5551STSB/), [IGVFFI6478TGPB](/sequence-files/IGVFFI6478TGPB/), [IGVFFI7830NIBI](/sequence-files/IGVFFI7830NIBI/), [IGVFFI6263BSHT](/sequence-files/IGVFFI6263BSHT/), [IGVFFI4296KZTZ](/sequence-files/IGVFFI4296KZTZ/), [IGVFFI1020OWEB](/sequence-files/IGVFFI1020OWEB/), [IGVFFI4791XXDL](/sequence-files/IGVFFI4791XXDL/), [IGVFFI1145KNZE](/sequence-files/IGVFFI1145KNZE/), [IGVFFI4402QMQD](/sequence-files/IGVFFI4402QMQD/), [IGVFFI9505ZJTP](/sequence-files/IGVFFI9505ZJTP/) 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/IGVFDS3158RHSP/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5856FZKF](/measurement-sets/IGVFDS5856FZKF/) 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/IGVFDS5856FZKF/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3158RHSP](/auxiliary-sets/IGVFDS3158RHSP/) has sequence file(s) [IGVFFI1815CRNJ](/sequence-files/IGVFFI1815CRNJ/), [IGVFFI2427CLUI](/sequence-files/IGVFFI2427CLUI/), [IGVFFI6845LMPY](/sequence-files/IGVFFI6845LMPY/), [IGVFFI5018WXNV](/sequence-files/IGVFFI5018WXNV/), [IGVFFI6397SUJC](/sequence-files/IGVFFI6397SUJC/), [IGVFFI3158RNKH](/sequence-files/IGVFFI3158RNKH/), [IGVFFI1282FWJQ](/sequence-files/IGVFFI1282FWJQ/), [IGVFFI7347GBNW](/sequence-files/IGVFFI7347GBNW/), [IGVFFI7734RLWM](/sequence-files/IGVFFI7734RLWM/), [IGVFFI5742CFJG](/sequence-files/IGVFFI5742CFJG/), [IGVFFI2823RWAW](/sequence-files/IGVFFI2823RWAW/), [IGVFFI3463QFUD](/sequence-files/IGVFFI3463QFUD/), [IGVFFI4047BBPJ](/sequence-files/IGVFFI4047BBPJ/), [IGVFFI3260ODND](/sequence-files/IGVFFI3260ODND/), [IGVFFI9237NRDU](/sequence-files/IGVFFI9237NRDU/), [IGVFFI7199EJUV](/sequence-files/IGVFFI7199EJUV/), [IGVFFI6029OCBI](/sequence-files/IGVFFI6029OCBI/), [IGVFFI1070KTCG](/sequence-files/IGVFFI1070KTCG/), [IGVFFI0578DORF](/sequence-files/IGVFFI0578DORF/), [IGVFFI9545EZRY](/sequence-files/IGVFFI9545EZRY/), [IGVFFI4721AXTO](/sequence-files/IGVFFI4721AXTO/), [IGVFFI1458HQEB](/sequence-files/IGVFFI1458HQEB/), [IGVFFI1130XONB](/sequence-files/IGVFFI1130XONB/), [IGVFFI4075FCRP](/sequence-files/IGVFFI4075FCRP/), [IGVFFI7502LMVQ](/sequence-files/IGVFFI7502LMVQ/), [IGVFFI3549ITFF](/sequence-files/IGVFFI3549ITFF/), [IGVFFI2031SKIL](/sequence-files/IGVFFI2031SKIL/), [IGVFFI2351TLFO](/sequence-files/IGVFFI2351TLFO/), [IGVFFI2520CEXS](/sequence-files/IGVFFI2520CEXS/), [IGVFFI6735AEPI](/sequence-files/IGVFFI6735AEPI/), [IGVFFI6748XRYL](/sequence-files/IGVFFI6748XRYL/), [IGVFFI1560IQYJ](/sequence-files/IGVFFI1560IQYJ/), [IGVFFI4859XPET](/sequence-files/IGVFFI4859XPET/), [IGVFFI6533YLMJ](/sequence-files/IGVFFI6533YLMJ/), [IGVFFI1023NAVB](/sequence-files/IGVFFI1023NAVB/), [IGVFFI7429CIJF](/sequence-files/IGVFFI7429CIJF/), [IGVFFI7113WZPT](/sequence-files/IGVFFI7113WZPT/), [IGVFFI0683KABS](/sequence-files/IGVFFI0683KABS/), [IGVFFI5551STSB](/sequence-files/IGVFFI5551STSB/), [IGVFFI6478TGPB](/sequence-files/IGVFFI6478TGPB/), [IGVFFI7830NIBI](/sequence-files/IGVFFI7830NIBI/), [IGVFFI6263BSHT](/sequence-files/IGVFFI6263BSHT/), [IGVFFI4296KZTZ](/sequence-files/IGVFFI4296KZTZ/), [IGVFFI1020OWEB](/sequence-files/IGVFFI1020OWEB/), [IGVFFI4791XXDL](/sequence-files/IGVFFI4791XXDL/), [IGVFFI1145KNZE](/sequence-files/IGVFFI1145KNZE/), [IGVFFI4402QMQD](/sequence-files/IGVFFI4402QMQD/), [IGVFFI9505ZJTP](/sequence-files/IGVFFI9505ZJTP/) 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/IGVFDS3158RHSP/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3158RHSP](/auxiliary-sets/IGVFDS3158RHSP/) 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/IGVFDS3158RHSP/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3158RHSP/",
"accession": "IGVFDS3158RHSP",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-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": "2023-12-13T08:48:11.854861+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": "2023-12-20T23:08:41.966536+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7961LTZR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7961LTZR",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-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": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T10:08:31.141544+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": "6c8ecad6-445f-4b0a-b1ab-aea54add7456"
}