{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7403HHLV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7403HHLV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinC_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 [IGVFDS7403HHLV](/measurement-sets/IGVFDS7403HHLV/) has in progress subobject auxiliary set [IGVFDS0582OVRW](/auxiliary-sets/IGVFDS0582OVRW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7403HHLV/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4383GTZM](/in-vitro-systems/IGVFSM4383GTZM/) 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/IGVFSM4383GTZM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7403HHLV](/measurement-sets/IGVFDS7403HHLV/) 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/IGVFDS7403HHLV/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0582OVRW](/auxiliary-sets/IGVFDS0582OVRW/) has sequence file(s) [IGVFFI4568EMWF](/sequence-files/IGVFFI4568EMWF/), [IGVFFI4126JRYP](/sequence-files/IGVFFI4126JRYP/), [IGVFFI9059CEVY](/sequence-files/IGVFFI9059CEVY/), [IGVFFI9905VMGC](/sequence-files/IGVFFI9905VMGC/), [IGVFFI0927NXPV](/sequence-files/IGVFFI0927NXPV/), [IGVFFI2174TQBM](/sequence-files/IGVFFI2174TQBM/), [IGVFFI3673JWHX](/sequence-files/IGVFFI3673JWHX/), [IGVFFI6225GLFN](/sequence-files/IGVFFI6225GLFN/), [IGVFFI5846LIZE](/sequence-files/IGVFFI5846LIZE/), [IGVFFI1932APVQ](/sequence-files/IGVFFI1932APVQ/), [IGVFFI7370QYEK](/sequence-files/IGVFFI7370QYEK/), [IGVFFI3214JGEH](/sequence-files/IGVFFI3214JGEH/), [IGVFFI0945EJMP](/sequence-files/IGVFFI0945EJMP/), [IGVFFI7181WODT](/sequence-files/IGVFFI7181WODT/), [IGVFFI3233UQOL](/sequence-files/IGVFFI3233UQOL/), [IGVFFI8214EBRF](/sequence-files/IGVFFI8214EBRF/), [IGVFFI1409URYL](/sequence-files/IGVFFI1409URYL/), [IGVFFI1261XJCS](/sequence-files/IGVFFI1261XJCS/), [IGVFFI0225FNQX](/sequence-files/IGVFFI0225FNQX/), [IGVFFI2842EDJI](/sequence-files/IGVFFI2842EDJI/), [IGVFFI2776LTMW](/sequence-files/IGVFFI2776LTMW/), [IGVFFI7494KNPP](/sequence-files/IGVFFI7494KNPP/), [IGVFFI1960GGTO](/sequence-files/IGVFFI1960GGTO/), [IGVFFI7346XVXB](/sequence-files/IGVFFI7346XVXB/), [IGVFFI7930PLEW](/sequence-files/IGVFFI7930PLEW/), [IGVFFI6541JGFZ](/sequence-files/IGVFFI6541JGFZ/), [IGVFFI4957DKGR](/sequence-files/IGVFFI4957DKGR/), [IGVFFI6230OQLR](/sequence-files/IGVFFI6230OQLR/), [IGVFFI5402XMEI](/sequence-files/IGVFFI5402XMEI/), [IGVFFI4346HMWL](/sequence-files/IGVFFI4346HMWL/), [IGVFFI1867GVHT](/sequence-files/IGVFFI1867GVHT/), [IGVFFI3420CNBD](/sequence-files/IGVFFI3420CNBD/), [IGVFFI7889TNAF](/sequence-files/IGVFFI7889TNAF/), [IGVFFI4426OOFF](/sequence-files/IGVFFI4426OOFF/), [IGVFFI4683OAAI](/sequence-files/IGVFFI4683OAAI/), [IGVFFI1608JBBS](/sequence-files/IGVFFI1608JBBS/), [IGVFFI7237DJRH](/sequence-files/IGVFFI7237DJRH/), [IGVFFI2538CSOH](/sequence-files/IGVFFI2538CSOH/), [IGVFFI7064HJJK](/sequence-files/IGVFFI7064HJJK/), [IGVFFI8912ZZEC](/sequence-files/IGVFFI8912ZZEC/), [IGVFFI7356JDYX](/sequence-files/IGVFFI7356JDYX/), [IGVFFI0664MBPI](/sequence-files/IGVFFI0664MBPI/), [IGVFFI1972HVMR](/sequence-files/IGVFFI1972HVMR/), [IGVFFI2152KHXJ](/sequence-files/IGVFFI2152KHXJ/), [IGVFFI0813LGQI](/sequence-files/IGVFFI0813LGQI/), [IGVFFI6753LWKP](/sequence-files/IGVFFI6753LWKP/), [IGVFFI0284ZTNM](/sequence-files/IGVFFI0284ZTNM/), [IGVFFI6438LITQ](/sequence-files/IGVFFI6438LITQ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0582OVRW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0582OVRW](/auxiliary-sets/IGVFDS0582OVRW/) has sequence file(s): [IGVFFI4568EMWF](/sequence-files/IGVFFI4568EMWF/), [IGVFFI4126JRYP](/sequence-files/IGVFFI4126JRYP/), [IGVFFI9059CEVY](/sequence-files/IGVFFI9059CEVY/), [IGVFFI9905VMGC](/sequence-files/IGVFFI9905VMGC/), [IGVFFI0927NXPV](/sequence-files/IGVFFI0927NXPV/), [IGVFFI2174TQBM](/sequence-files/IGVFFI2174TQBM/), [IGVFFI3673JWHX](/sequence-files/IGVFFI3673JWHX/), [IGVFFI6225GLFN](/sequence-files/IGVFFI6225GLFN/), [IGVFFI5846LIZE](/sequence-files/IGVFFI5846LIZE/), [IGVFFI1932APVQ](/sequence-files/IGVFFI1932APVQ/), [IGVFFI7370QYEK](/sequence-files/IGVFFI7370QYEK/), [IGVFFI3214JGEH](/sequence-files/IGVFFI3214JGEH/), [IGVFFI0945EJMP](/sequence-files/IGVFFI0945EJMP/), [IGVFFI7181WODT](/sequence-files/IGVFFI7181WODT/), [IGVFFI3233UQOL](/sequence-files/IGVFFI3233UQOL/), [IGVFFI8214EBRF](/sequence-files/IGVFFI8214EBRF/), [IGVFFI1409URYL](/sequence-files/IGVFFI1409URYL/), [IGVFFI1261XJCS](/sequence-files/IGVFFI1261XJCS/), [IGVFFI0225FNQX](/sequence-files/IGVFFI0225FNQX/), [IGVFFI2842EDJI](/sequence-files/IGVFFI2842EDJI/), [IGVFFI2776LTMW](/sequence-files/IGVFFI2776LTMW/), [IGVFFI7494KNPP](/sequence-files/IGVFFI7494KNPP/), [IGVFFI1960GGTO](/sequence-files/IGVFFI1960GGTO/), [IGVFFI7346XVXB](/sequence-files/IGVFFI7346XVXB/), [IGVFFI7930PLEW](/sequence-files/IGVFFI7930PLEW/), [IGVFFI6541JGFZ](/sequence-files/IGVFFI6541JGFZ/), [IGVFFI4957DKGR](/sequence-files/IGVFFI4957DKGR/), [IGVFFI6230OQLR](/sequence-files/IGVFFI6230OQLR/), [IGVFFI5402XMEI](/sequence-files/IGVFFI5402XMEI/), [IGVFFI4346HMWL](/sequence-files/IGVFFI4346HMWL/), [IGVFFI1867GVHT](/sequence-files/IGVFFI1867GVHT/), [IGVFFI3420CNBD](/sequence-files/IGVFFI3420CNBD/), [IGVFFI7889TNAF](/sequence-files/IGVFFI7889TNAF/), [IGVFFI4426OOFF](/sequence-files/IGVFFI4426OOFF/), [IGVFFI4683OAAI](/sequence-files/IGVFFI4683OAAI/), [IGVFFI1608JBBS](/sequence-files/IGVFFI1608JBBS/), [IGVFFI7237DJRH](/sequence-files/IGVFFI7237DJRH/), [IGVFFI2538CSOH](/sequence-files/IGVFFI2538CSOH/), [IGVFFI7064HJJK](/sequence-files/IGVFFI7064HJJK/), [IGVFFI8912ZZEC](/sequence-files/IGVFFI8912ZZEC/), [IGVFFI7356JDYX](/sequence-files/IGVFFI7356JDYX/), [IGVFFI0664MBPI](/sequence-files/IGVFFI0664MBPI/), [IGVFFI1972HVMR](/sequence-files/IGVFFI1972HVMR/), [IGVFFI2152KHXJ](/sequence-files/IGVFFI2152KHXJ/), [IGVFFI0813LGQI](/sequence-files/IGVFFI0813LGQI/), [IGVFFI6753LWKP](/sequence-files/IGVFFI6753LWKP/), [IGVFFI0284ZTNM](/sequence-files/IGVFFI0284ZTNM/), [IGVFFI6438LITQ](/sequence-files/IGVFFI6438LITQ/) 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/IGVFDS0582OVRW/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0582OVRW](/auxiliary-sets/IGVFDS0582OVRW/) 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_for",
"path": "/auxiliary-sets/IGVFDS0582OVRW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0582OVRW/",
"accession": "IGVFDS0582OVRW",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinC_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": "2023-11-30T22:49:38.741792+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_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": "2023-12-20T23:06:45.655094+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4383GTZM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4383GTZM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinC"
],
"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 51-75% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T20:15:09.454485+00:00",
"summary": "prime editing 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": "e0bd4ba1-42ff-4e27-8046-6193ef27b766"
}