{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9080CILW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9080CILW",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep2-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 [IGVFDS9080CILW](/measurement-sets/IGVFDS9080CILW/) has in progress subobject auxiliary set [IGVFDS6646TUYY](/auxiliary-sets/IGVFDS6646TUYY/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9080CILW/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9682UDFK](/in-vitro-systems/IGVFSM9682UDFK/) 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/IGVFSM9682UDFK/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9080CILW](/measurement-sets/IGVFDS9080CILW/) 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/IGVFDS9080CILW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6646TUYY](/auxiliary-sets/IGVFDS6646TUYY/) has sequence file(s): [IGVFFI8239KYGI](/sequence-files/IGVFFI8239KYGI/), [IGVFFI8517DEBM](/sequence-files/IGVFFI8517DEBM/), [IGVFFI2777SWYW](/sequence-files/IGVFFI2777SWYW/), [IGVFFI0301XWXP](/sequence-files/IGVFFI0301XWXP/), [IGVFFI8102YJHH](/sequence-files/IGVFFI8102YJHH/), [IGVFFI2290PFOF](/sequence-files/IGVFFI2290PFOF/), [IGVFFI3887XUHJ](/sequence-files/IGVFFI3887XUHJ/), [IGVFFI9077FLFQ](/sequence-files/IGVFFI9077FLFQ/), [IGVFFI9970EBKS](/sequence-files/IGVFFI9970EBKS/), [IGVFFI5268OCZE](/sequence-files/IGVFFI5268OCZE/), [IGVFFI6725YAKE](/sequence-files/IGVFFI6725YAKE/), [IGVFFI9857GLTM](/sequence-files/IGVFFI9857GLTM/), [IGVFFI9588DRGV](/sequence-files/IGVFFI9588DRGV/), [IGVFFI6943NLVX](/sequence-files/IGVFFI6943NLVX/), [IGVFFI9729UPTH](/sequence-files/IGVFFI9729UPTH/), [IGVFFI6965TRNF](/sequence-files/IGVFFI6965TRNF/), [IGVFFI8171WIRK](/sequence-files/IGVFFI8171WIRK/), [IGVFFI5138PGXZ](/sequence-files/IGVFFI5138PGXZ/), [IGVFFI7773FRKU](/sequence-files/IGVFFI7773FRKU/), [IGVFFI8387JJGS](/sequence-files/IGVFFI8387JJGS/), [IGVFFI0965VKXK](/sequence-files/IGVFFI0965VKXK/), [IGVFFI1660TKRZ](/sequence-files/IGVFFI1660TKRZ/), [IGVFFI1528OAKE](/sequence-files/IGVFFI1528OAKE/), [IGVFFI7855EYVT](/sequence-files/IGVFFI7855EYVT/), [IGVFFI8103TUQD](/sequence-files/IGVFFI8103TUQD/), [IGVFFI6978CSMX](/sequence-files/IGVFFI6978CSMX/), [IGVFFI2340ACGJ](/sequence-files/IGVFFI2340ACGJ/), [IGVFFI1914GPLU](/sequence-files/IGVFFI1914GPLU/), [IGVFFI2734EQMX](/sequence-files/IGVFFI2734EQMX/), [IGVFFI6911LHPR](/sequence-files/IGVFFI6911LHPR/), [IGVFFI6466OUUC](/sequence-files/IGVFFI6466OUUC/), [IGVFFI3026SPYK](/sequence-files/IGVFFI3026SPYK/), [IGVFFI7007URDN](/sequence-files/IGVFFI7007URDN/), [IGVFFI7618CLSB](/sequence-files/IGVFFI7618CLSB/), [IGVFFI6225EMSE](/sequence-files/IGVFFI6225EMSE/), [IGVFFI5958TAXN](/sequence-files/IGVFFI5958TAXN/), [IGVFFI4489LORS](/sequence-files/IGVFFI4489LORS/), [IGVFFI1771JIAJ](/sequence-files/IGVFFI1771JIAJ/), [IGVFFI2536UMHT](/sequence-files/IGVFFI2536UMHT/), [IGVFFI9548OWQS](/sequence-files/IGVFFI9548OWQS/), [IGVFFI0291WWOF](/sequence-files/IGVFFI0291WWOF/), [IGVFFI4313OJHH](/sequence-files/IGVFFI4313OJHH/), [IGVFFI2209NQUW](/sequence-files/IGVFFI2209NQUW/), [IGVFFI0784JLER](/sequence-files/IGVFFI0784JLER/), [IGVFFI2780WSBU](/sequence-files/IGVFFI2780WSBU/), [IGVFFI5745TWPY](/sequence-files/IGVFFI5745TWPY/), [IGVFFI4105XFFR](/sequence-files/IGVFFI4105XFFR/), [IGVFFI9638URWZ](/sequence-files/IGVFFI9638URWZ/) 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/IGVFDS6646TUYY/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6646TUYY](/auxiliary-sets/IGVFDS6646TUYY/) has sequence file(s) [IGVFFI8239KYGI](/sequence-files/IGVFFI8239KYGI/), [IGVFFI8517DEBM](/sequence-files/IGVFFI8517DEBM/), [IGVFFI2777SWYW](/sequence-files/IGVFFI2777SWYW/), [IGVFFI0301XWXP](/sequence-files/IGVFFI0301XWXP/), [IGVFFI8102YJHH](/sequence-files/IGVFFI8102YJHH/), [IGVFFI2290PFOF](/sequence-files/IGVFFI2290PFOF/), [IGVFFI3887XUHJ](/sequence-files/IGVFFI3887XUHJ/), [IGVFFI9077FLFQ](/sequence-files/IGVFFI9077FLFQ/), [IGVFFI9970EBKS](/sequence-files/IGVFFI9970EBKS/), [IGVFFI5268OCZE](/sequence-files/IGVFFI5268OCZE/), [IGVFFI6725YAKE](/sequence-files/IGVFFI6725YAKE/), [IGVFFI9857GLTM](/sequence-files/IGVFFI9857GLTM/), [IGVFFI9588DRGV](/sequence-files/IGVFFI9588DRGV/), [IGVFFI6943NLVX](/sequence-files/IGVFFI6943NLVX/), [IGVFFI9729UPTH](/sequence-files/IGVFFI9729UPTH/), [IGVFFI6965TRNF](/sequence-files/IGVFFI6965TRNF/), [IGVFFI8171WIRK](/sequence-files/IGVFFI8171WIRK/), [IGVFFI5138PGXZ](/sequence-files/IGVFFI5138PGXZ/), [IGVFFI7773FRKU](/sequence-files/IGVFFI7773FRKU/), [IGVFFI8387JJGS](/sequence-files/IGVFFI8387JJGS/), [IGVFFI0965VKXK](/sequence-files/IGVFFI0965VKXK/), [IGVFFI1660TKRZ](/sequence-files/IGVFFI1660TKRZ/), [IGVFFI1528OAKE](/sequence-files/IGVFFI1528OAKE/), [IGVFFI7855EYVT](/sequence-files/IGVFFI7855EYVT/), [IGVFFI8103TUQD](/sequence-files/IGVFFI8103TUQD/), [IGVFFI6978CSMX](/sequence-files/IGVFFI6978CSMX/), [IGVFFI2340ACGJ](/sequence-files/IGVFFI2340ACGJ/), [IGVFFI1914GPLU](/sequence-files/IGVFFI1914GPLU/), [IGVFFI2734EQMX](/sequence-files/IGVFFI2734EQMX/), [IGVFFI6911LHPR](/sequence-files/IGVFFI6911LHPR/), [IGVFFI6466OUUC](/sequence-files/IGVFFI6466OUUC/), [IGVFFI3026SPYK](/sequence-files/IGVFFI3026SPYK/), [IGVFFI7007URDN](/sequence-files/IGVFFI7007URDN/), [IGVFFI7618CLSB](/sequence-files/IGVFFI7618CLSB/), [IGVFFI6225EMSE](/sequence-files/IGVFFI6225EMSE/), [IGVFFI5958TAXN](/sequence-files/IGVFFI5958TAXN/), [IGVFFI4489LORS](/sequence-files/IGVFFI4489LORS/), [IGVFFI1771JIAJ](/sequence-files/IGVFFI1771JIAJ/), [IGVFFI2536UMHT](/sequence-files/IGVFFI2536UMHT/), [IGVFFI9548OWQS](/sequence-files/IGVFFI9548OWQS/), [IGVFFI0291WWOF](/sequence-files/IGVFFI0291WWOF/), [IGVFFI4313OJHH](/sequence-files/IGVFFI4313OJHH/), [IGVFFI2209NQUW](/sequence-files/IGVFFI2209NQUW/), [IGVFFI0784JLER](/sequence-files/IGVFFI0784JLER/), [IGVFFI2780WSBU](/sequence-files/IGVFFI2780WSBU/), [IGVFFI5745TWPY](/sequence-files/IGVFFI5745TWPY/), [IGVFFI4105XFFR](/sequence-files/IGVFFI4105XFFR/), [IGVFFI9638URWZ](/sequence-files/IGVFFI9638URWZ/) 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/IGVFDS6646TUYY/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6646TUYY](/auxiliary-sets/IGVFDS6646TUYY/) 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/IGVFDS6646TUYY/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6646TUYY/",
"accession": "IGVFDS6646TUYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep2-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": "2023-12-13T08:48:12.412120+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": "2023-12-20T23:08:15.792663+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9682UDFK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9682UDFK",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep2-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": "2023-12-13T10:08:50.257279+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": "718b62e6-a01c-4a01-b802-98e4a09c0f68"
}