{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3532HUSQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3532HUSQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-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 [IGVFDS3532HUSQ](/measurement-sets/IGVFDS3532HUSQ/) has in progress subobject auxiliary set [IGVFDS1380YACC](/auxiliary-sets/IGVFDS1380YACC/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3532HUSQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6349GRPM](/in-vitro-systems/IGVFSM6349GRPM/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6349GRPM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3532HUSQ](/measurement-sets/IGVFDS3532HUSQ/) 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/IGVFDS3532HUSQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1380YACC](/auxiliary-sets/IGVFDS1380YACC/) has sequence file(s): [IGVFFI9011JZSP](/sequence-files/IGVFFI9011JZSP/), [IGVFFI6234VYOB](/sequence-files/IGVFFI6234VYOB/), [IGVFFI3373KOZN](/sequence-files/IGVFFI3373KOZN/), [IGVFFI5134PITR](/sequence-files/IGVFFI5134PITR/), [IGVFFI6368TQSJ](/sequence-files/IGVFFI6368TQSJ/), [IGVFFI4202SXOX](/sequence-files/IGVFFI4202SXOX/), [IGVFFI2450ULEZ](/sequence-files/IGVFFI2450ULEZ/), [IGVFFI9425XFLN](/sequence-files/IGVFFI9425XFLN/), [IGVFFI7697CPHD](/sequence-files/IGVFFI7697CPHD/), [IGVFFI6303CIJR](/sequence-files/IGVFFI6303CIJR/), [IGVFFI2645LXDJ](/sequence-files/IGVFFI2645LXDJ/), [IGVFFI4708YAVO](/sequence-files/IGVFFI4708YAVO/), [IGVFFI5937UKNN](/sequence-files/IGVFFI5937UKNN/), [IGVFFI7637WAPF](/sequence-files/IGVFFI7637WAPF/), [IGVFFI3983GSVX](/sequence-files/IGVFFI3983GSVX/), [IGVFFI3648SBAZ](/sequence-files/IGVFFI3648SBAZ/), [IGVFFI4499KBGC](/sequence-files/IGVFFI4499KBGC/), [IGVFFI5093CIBV](/sequence-files/IGVFFI5093CIBV/), [IGVFFI5717NMGE](/sequence-files/IGVFFI5717NMGE/), [IGVFFI8226JTAF](/sequence-files/IGVFFI8226JTAF/), [IGVFFI7953IKDE](/sequence-files/IGVFFI7953IKDE/), [IGVFFI0505WQCE](/sequence-files/IGVFFI0505WQCE/), [IGVFFI2608UIFP](/sequence-files/IGVFFI2608UIFP/), [IGVFFI3892YYBS](/sequence-files/IGVFFI3892YYBS/), [IGVFFI6430CSSG](/sequence-files/IGVFFI6430CSSG/), [IGVFFI6740EQGP](/sequence-files/IGVFFI6740EQGP/), [IGVFFI9902DTNW](/sequence-files/IGVFFI9902DTNW/), [IGVFFI8167CDYG](/sequence-files/IGVFFI8167CDYG/), [IGVFFI7788LKMY](/sequence-files/IGVFFI7788LKMY/), [IGVFFI1380XBAY](/sequence-files/IGVFFI1380XBAY/), [IGVFFI9480LVQQ](/sequence-files/IGVFFI9480LVQQ/), [IGVFFI5997HFUY](/sequence-files/IGVFFI5997HFUY/), [IGVFFI2693TTKH](/sequence-files/IGVFFI2693TTKH/), [IGVFFI1757ZMTH](/sequence-files/IGVFFI1757ZMTH/), [IGVFFI4336OOGL](/sequence-files/IGVFFI4336OOGL/), [IGVFFI2668LZJW](/sequence-files/IGVFFI2668LZJW/), [IGVFFI7852SUZC](/sequence-files/IGVFFI7852SUZC/), [IGVFFI2203XIZT](/sequence-files/IGVFFI2203XIZT/), [IGVFFI4961ENEV](/sequence-files/IGVFFI4961ENEV/), [IGVFFI7847SIPQ](/sequence-files/IGVFFI7847SIPQ/), [IGVFFI8035JAYZ](/sequence-files/IGVFFI8035JAYZ/), [IGVFFI7865JYFJ](/sequence-files/IGVFFI7865JYFJ/), [IGVFFI0892EAHG](/sequence-files/IGVFFI0892EAHG/), [IGVFFI3895LVSP](/sequence-files/IGVFFI3895LVSP/), [IGVFFI5236DVMS](/sequence-files/IGVFFI5236DVMS/), [IGVFFI2828PORV](/sequence-files/IGVFFI2828PORV/), [IGVFFI3015OBRV](/sequence-files/IGVFFI3015OBRV/), [IGVFFI2640KDXP](/sequence-files/IGVFFI2640KDXP/) 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/IGVFDS1380YACC/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1380YACC](/auxiliary-sets/IGVFDS1380YACC/) has sequence file(s) [IGVFFI9011JZSP](/sequence-files/IGVFFI9011JZSP/), [IGVFFI6234VYOB](/sequence-files/IGVFFI6234VYOB/), [IGVFFI3373KOZN](/sequence-files/IGVFFI3373KOZN/), [IGVFFI5134PITR](/sequence-files/IGVFFI5134PITR/), [IGVFFI6368TQSJ](/sequence-files/IGVFFI6368TQSJ/), [IGVFFI4202SXOX](/sequence-files/IGVFFI4202SXOX/), [IGVFFI2450ULEZ](/sequence-files/IGVFFI2450ULEZ/), [IGVFFI9425XFLN](/sequence-files/IGVFFI9425XFLN/), [IGVFFI7697CPHD](/sequence-files/IGVFFI7697CPHD/), [IGVFFI6303CIJR](/sequence-files/IGVFFI6303CIJR/), [IGVFFI2645LXDJ](/sequence-files/IGVFFI2645LXDJ/), [IGVFFI4708YAVO](/sequence-files/IGVFFI4708YAVO/), [IGVFFI5937UKNN](/sequence-files/IGVFFI5937UKNN/), [IGVFFI7637WAPF](/sequence-files/IGVFFI7637WAPF/), [IGVFFI3983GSVX](/sequence-files/IGVFFI3983GSVX/), [IGVFFI3648SBAZ](/sequence-files/IGVFFI3648SBAZ/), [IGVFFI4499KBGC](/sequence-files/IGVFFI4499KBGC/), [IGVFFI5093CIBV](/sequence-files/IGVFFI5093CIBV/), [IGVFFI5717NMGE](/sequence-files/IGVFFI5717NMGE/), [IGVFFI8226JTAF](/sequence-files/IGVFFI8226JTAF/), [IGVFFI7953IKDE](/sequence-files/IGVFFI7953IKDE/), [IGVFFI0505WQCE](/sequence-files/IGVFFI0505WQCE/), [IGVFFI2608UIFP](/sequence-files/IGVFFI2608UIFP/), [IGVFFI3892YYBS](/sequence-files/IGVFFI3892YYBS/), [IGVFFI6430CSSG](/sequence-files/IGVFFI6430CSSG/), [IGVFFI6740EQGP](/sequence-files/IGVFFI6740EQGP/), [IGVFFI9902DTNW](/sequence-files/IGVFFI9902DTNW/), [IGVFFI8167CDYG](/sequence-files/IGVFFI8167CDYG/), [IGVFFI7788LKMY](/sequence-files/IGVFFI7788LKMY/), [IGVFFI1380XBAY](/sequence-files/IGVFFI1380XBAY/), [IGVFFI9480LVQQ](/sequence-files/IGVFFI9480LVQQ/), [IGVFFI5997HFUY](/sequence-files/IGVFFI5997HFUY/), [IGVFFI2693TTKH](/sequence-files/IGVFFI2693TTKH/), [IGVFFI1757ZMTH](/sequence-files/IGVFFI1757ZMTH/), [IGVFFI4336OOGL](/sequence-files/IGVFFI4336OOGL/), [IGVFFI2668LZJW](/sequence-files/IGVFFI2668LZJW/), [IGVFFI7852SUZC](/sequence-files/IGVFFI7852SUZC/), [IGVFFI2203XIZT](/sequence-files/IGVFFI2203XIZT/), [IGVFFI4961ENEV](/sequence-files/IGVFFI4961ENEV/), [IGVFFI7847SIPQ](/sequence-files/IGVFFI7847SIPQ/), [IGVFFI8035JAYZ](/sequence-files/IGVFFI8035JAYZ/), [IGVFFI7865JYFJ](/sequence-files/IGVFFI7865JYFJ/), [IGVFFI0892EAHG](/sequence-files/IGVFFI0892EAHG/), [IGVFFI3895LVSP](/sequence-files/IGVFFI3895LVSP/), [IGVFFI5236DVMS](/sequence-files/IGVFFI5236DVMS/), [IGVFFI2828PORV](/sequence-files/IGVFFI2828PORV/), [IGVFFI3015OBRV](/sequence-files/IGVFFI3015OBRV/), [IGVFFI2640KDXP](/sequence-files/IGVFFI2640KDXP/) 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/IGVFDS1380YACC/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1380YACC](/auxiliary-sets/IGVFDS1380YACC/) 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/IGVFDS1380YACC/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1380YACC/",
"accession": "IGVFDS1380YACC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:50:13.806889+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:53.050655+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6349GRPM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6349GRPM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 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": "2023-12-05T23:18:42.492326+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": "b04f2097-2568-42fe-8a02-f703247ea289"
}