{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5913KHIA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5913KHIA",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-BinD_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 [IGVFDS5913KHIA](/measurement-sets/IGVFDS5913KHIA/) has in progress subobject auxiliary set [IGVFDS6460GMYB](/auxiliary-sets/IGVFDS6460GMYB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5913KHIA/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7851LWAO](/in-vitro-systems/IGVFSM7851LWAO/) 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/IGVFSM7851LWAO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5913KHIA](/measurement-sets/IGVFDS5913KHIA/) 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/IGVFDS5913KHIA/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6460GMYB](/auxiliary-sets/IGVFDS6460GMYB/) has sequence file(s): [IGVFFI5452CYWL](/sequence-files/IGVFFI5452CYWL/), [IGVFFI6655JAPW](/sequence-files/IGVFFI6655JAPW/), [IGVFFI4421QDTT](/sequence-files/IGVFFI4421QDTT/), [IGVFFI5818VNBR](/sequence-files/IGVFFI5818VNBR/), [IGVFFI9608GESS](/sequence-files/IGVFFI9608GESS/), [IGVFFI5294JVMX](/sequence-files/IGVFFI5294JVMX/), [IGVFFI7920HFLI](/sequence-files/IGVFFI7920HFLI/), [IGVFFI9480YDCO](/sequence-files/IGVFFI9480YDCO/), [IGVFFI7341HWPH](/sequence-files/IGVFFI7341HWPH/), [IGVFFI3811KSQC](/sequence-files/IGVFFI3811KSQC/), [IGVFFI7873OIUE](/sequence-files/IGVFFI7873OIUE/), [IGVFFI3012YXAK](/sequence-files/IGVFFI3012YXAK/), [IGVFFI7938MENJ](/sequence-files/IGVFFI7938MENJ/), [IGVFFI4177KYYC](/sequence-files/IGVFFI4177KYYC/), [IGVFFI1303ZTTN](/sequence-files/IGVFFI1303ZTTN/), [IGVFFI7359WYQF](/sequence-files/IGVFFI7359WYQF/), [IGVFFI6386ZUWN](/sequence-files/IGVFFI6386ZUWN/), [IGVFFI4463IBNY](/sequence-files/IGVFFI4463IBNY/), [IGVFFI7684KIMI](/sequence-files/IGVFFI7684KIMI/), [IGVFFI1810TZQV](/sequence-files/IGVFFI1810TZQV/), [IGVFFI1913FFQJ](/sequence-files/IGVFFI1913FFQJ/), [IGVFFI3756ANLH](/sequence-files/IGVFFI3756ANLH/), [IGVFFI1558GVUC](/sequence-files/IGVFFI1558GVUC/), [IGVFFI1108PSAW](/sequence-files/IGVFFI1108PSAW/), [IGVFFI4316PKDA](/sequence-files/IGVFFI4316PKDA/), [IGVFFI9825BHGE](/sequence-files/IGVFFI9825BHGE/), [IGVFFI2241FYTJ](/sequence-files/IGVFFI2241FYTJ/), [IGVFFI2156MITI](/sequence-files/IGVFFI2156MITI/), [IGVFFI5672UYDO](/sequence-files/IGVFFI5672UYDO/), [IGVFFI8096EASF](/sequence-files/IGVFFI8096EASF/), [IGVFFI3327HAOS](/sequence-files/IGVFFI3327HAOS/), [IGVFFI3399PZOV](/sequence-files/IGVFFI3399PZOV/), [IGVFFI7851RHVZ](/sequence-files/IGVFFI7851RHVZ/), [IGVFFI2894ZQGP](/sequence-files/IGVFFI2894ZQGP/), [IGVFFI8253WUCT](/sequence-files/IGVFFI8253WUCT/), [IGVFFI2978PYSU](/sequence-files/IGVFFI2978PYSU/), [IGVFFI4627LCPN](/sequence-files/IGVFFI4627LCPN/), [IGVFFI9468LANJ](/sequence-files/IGVFFI9468LANJ/), [IGVFFI9486WWEX](/sequence-files/IGVFFI9486WWEX/), [IGVFFI5359OUPB](/sequence-files/IGVFFI5359OUPB/), [IGVFFI5087YCLK](/sequence-files/IGVFFI5087YCLK/), [IGVFFI6967WIEV](/sequence-files/IGVFFI6967WIEV/), [IGVFFI8359MZAM](/sequence-files/IGVFFI8359MZAM/), [IGVFFI5550ZWCR](/sequence-files/IGVFFI5550ZWCR/), [IGVFFI4078ESRZ](/sequence-files/IGVFFI4078ESRZ/), [IGVFFI9807EPBQ](/sequence-files/IGVFFI9807EPBQ/), [IGVFFI2359IDCS](/sequence-files/IGVFFI2359IDCS/), [IGVFFI1752QHPB](/sequence-files/IGVFFI1752QHPB/) 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/IGVFDS6460GMYB/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6460GMYB](/auxiliary-sets/IGVFDS6460GMYB/) has sequence file(s) [IGVFFI5452CYWL](/sequence-files/IGVFFI5452CYWL/), [IGVFFI6655JAPW](/sequence-files/IGVFFI6655JAPW/), [IGVFFI4421QDTT](/sequence-files/IGVFFI4421QDTT/), [IGVFFI5818VNBR](/sequence-files/IGVFFI5818VNBR/), [IGVFFI9608GESS](/sequence-files/IGVFFI9608GESS/), [IGVFFI5294JVMX](/sequence-files/IGVFFI5294JVMX/), [IGVFFI7920HFLI](/sequence-files/IGVFFI7920HFLI/), [IGVFFI9480YDCO](/sequence-files/IGVFFI9480YDCO/), [IGVFFI7341HWPH](/sequence-files/IGVFFI7341HWPH/), [IGVFFI3811KSQC](/sequence-files/IGVFFI3811KSQC/), [IGVFFI7873OIUE](/sequence-files/IGVFFI7873OIUE/), [IGVFFI3012YXAK](/sequence-files/IGVFFI3012YXAK/), [IGVFFI7938MENJ](/sequence-files/IGVFFI7938MENJ/), [IGVFFI4177KYYC](/sequence-files/IGVFFI4177KYYC/), [IGVFFI1303ZTTN](/sequence-files/IGVFFI1303ZTTN/), [IGVFFI7359WYQF](/sequence-files/IGVFFI7359WYQF/), [IGVFFI6386ZUWN](/sequence-files/IGVFFI6386ZUWN/), [IGVFFI4463IBNY](/sequence-files/IGVFFI4463IBNY/), [IGVFFI7684KIMI](/sequence-files/IGVFFI7684KIMI/), [IGVFFI1810TZQV](/sequence-files/IGVFFI1810TZQV/), [IGVFFI1913FFQJ](/sequence-files/IGVFFI1913FFQJ/), [IGVFFI3756ANLH](/sequence-files/IGVFFI3756ANLH/), [IGVFFI1558GVUC](/sequence-files/IGVFFI1558GVUC/), [IGVFFI1108PSAW](/sequence-files/IGVFFI1108PSAW/), [IGVFFI4316PKDA](/sequence-files/IGVFFI4316PKDA/), [IGVFFI9825BHGE](/sequence-files/IGVFFI9825BHGE/), [IGVFFI2241FYTJ](/sequence-files/IGVFFI2241FYTJ/), [IGVFFI2156MITI](/sequence-files/IGVFFI2156MITI/), [IGVFFI5672UYDO](/sequence-files/IGVFFI5672UYDO/), [IGVFFI8096EASF](/sequence-files/IGVFFI8096EASF/), [IGVFFI3327HAOS](/sequence-files/IGVFFI3327HAOS/), [IGVFFI3399PZOV](/sequence-files/IGVFFI3399PZOV/), [IGVFFI7851RHVZ](/sequence-files/IGVFFI7851RHVZ/), [IGVFFI2894ZQGP](/sequence-files/IGVFFI2894ZQGP/), [IGVFFI8253WUCT](/sequence-files/IGVFFI8253WUCT/), [IGVFFI2978PYSU](/sequence-files/IGVFFI2978PYSU/), [IGVFFI4627LCPN](/sequence-files/IGVFFI4627LCPN/), [IGVFFI9468LANJ](/sequence-files/IGVFFI9468LANJ/), [IGVFFI9486WWEX](/sequence-files/IGVFFI9486WWEX/), [IGVFFI5359OUPB](/sequence-files/IGVFFI5359OUPB/), [IGVFFI5087YCLK](/sequence-files/IGVFFI5087YCLK/), [IGVFFI6967WIEV](/sequence-files/IGVFFI6967WIEV/), [IGVFFI8359MZAM](/sequence-files/IGVFFI8359MZAM/), [IGVFFI5550ZWCR](/sequence-files/IGVFFI5550ZWCR/), [IGVFFI4078ESRZ](/sequence-files/IGVFFI4078ESRZ/), [IGVFFI9807EPBQ](/sequence-files/IGVFFI9807EPBQ/), [IGVFFI2359IDCS](/sequence-files/IGVFFI2359IDCS/), [IGVFFI1752QHPB](/sequence-files/IGVFFI1752QHPB/) 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/IGVFDS6460GMYB/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6460GMYB](/auxiliary-sets/IGVFDS6460GMYB/) 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/IGVFDS6460GMYB/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6460GMYB/",
"accession": "IGVFDS6460GMYB",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-BinD_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": "2023-12-13T08:48:07.279001+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": "2023-12-20T23:08:59.300108+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7851LWAO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7851LWAO",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-BinD"
],
"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 76-100% 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": "2023-12-13T09:44:53.986278+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": "42db5731-2679-4fd7-ae14-db542d2a36fb"
}