{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0176OXWE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0176OXWE",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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 measurement set [IGVFDS0176OXWE](/measurement-sets/IGVFDS0176OXWE/) has in progress subobject auxiliary set [IGVFDS2972LLXA](/auxiliary-sets/IGVFDS2972LLXA/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0176OXWE/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0694FDBK](/in-vitro-systems/IGVFSM0694FDBK/) 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/IGVFSM0694FDBK/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0176OXWE](/measurement-sets/IGVFDS0176OXWE/) 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/IGVFDS0176OXWE/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2972LLXA](/auxiliary-sets/IGVFDS2972LLXA/) has sequence file(s): [IGVFFI3079NZEG](/sequence-files/IGVFFI3079NZEG/), [IGVFFI7949SZEK](/sequence-files/IGVFFI7949SZEK/), [IGVFFI6666QLTV](/sequence-files/IGVFFI6666QLTV/), [IGVFFI8980JRKI](/sequence-files/IGVFFI8980JRKI/), [IGVFFI4337GCRP](/sequence-files/IGVFFI4337GCRP/), [IGVFFI2127ZLYL](/sequence-files/IGVFFI2127ZLYL/), [IGVFFI7754ICDD](/sequence-files/IGVFFI7754ICDD/), [IGVFFI5492LLUC](/sequence-files/IGVFFI5492LLUC/), [IGVFFI2508AAIU](/sequence-files/IGVFFI2508AAIU/), [IGVFFI4299MZIY](/sequence-files/IGVFFI4299MZIY/), [IGVFFI7025QNKP](/sequence-files/IGVFFI7025QNKP/), [IGVFFI9400RMGI](/sequence-files/IGVFFI9400RMGI/), [IGVFFI1875DXRD](/sequence-files/IGVFFI1875DXRD/), [IGVFFI3322MNRK](/sequence-files/IGVFFI3322MNRK/), [IGVFFI3780XPOL](/sequence-files/IGVFFI3780XPOL/), [IGVFFI2250TDFC](/sequence-files/IGVFFI2250TDFC/), [IGVFFI7927JOGR](/sequence-files/IGVFFI7927JOGR/), [IGVFFI7771RGUQ](/sequence-files/IGVFFI7771RGUQ/), [IGVFFI9785BXJQ](/sequence-files/IGVFFI9785BXJQ/), [IGVFFI7964MLAD](/sequence-files/IGVFFI7964MLAD/), [IGVFFI3684OAEZ](/sequence-files/IGVFFI3684OAEZ/), [IGVFFI8150MHSA](/sequence-files/IGVFFI8150MHSA/), [IGVFFI2067VNBK](/sequence-files/IGVFFI2067VNBK/), [IGVFFI3175IPAG](/sequence-files/IGVFFI3175IPAG/), [IGVFFI6653HVSW](/sequence-files/IGVFFI6653HVSW/), [IGVFFI8657NYAV](/sequence-files/IGVFFI8657NYAV/), [IGVFFI8157YIDD](/sequence-files/IGVFFI8157YIDD/), [IGVFFI5221VOBZ](/sequence-files/IGVFFI5221VOBZ/), [IGVFFI1355QYLF](/sequence-files/IGVFFI1355QYLF/), [IGVFFI1312RODU](/sequence-files/IGVFFI1312RODU/), [IGVFFI1259DZIX](/sequence-files/IGVFFI1259DZIX/), [IGVFFI5849MCSN](/sequence-files/IGVFFI5849MCSN/), [IGVFFI9204YAJH](/sequence-files/IGVFFI9204YAJH/), [IGVFFI9553HJAO](/sequence-files/IGVFFI9553HJAO/), [IGVFFI1740MSCJ](/sequence-files/IGVFFI1740MSCJ/), [IGVFFI1540YXCW](/sequence-files/IGVFFI1540YXCW/), [IGVFFI0985NIJF](/sequence-files/IGVFFI0985NIJF/), [IGVFFI0283YQAF](/sequence-files/IGVFFI0283YQAF/), [IGVFFI1095TZZN](/sequence-files/IGVFFI1095TZZN/), [IGVFFI5693ZVWI](/sequence-files/IGVFFI5693ZVWI/), [IGVFFI2572ASWX](/sequence-files/IGVFFI2572ASWX/), [IGVFFI6178SMTS](/sequence-files/IGVFFI6178SMTS/), [IGVFFI3821QRGY](/sequence-files/IGVFFI3821QRGY/), [IGVFFI3988BDGZ](/sequence-files/IGVFFI3988BDGZ/), [IGVFFI2419TMOK](/sequence-files/IGVFFI2419TMOK/), [IGVFFI7028HVED](/sequence-files/IGVFFI7028HVED/), [IGVFFI0642NPOT](/sequence-files/IGVFFI0642NPOT/), [IGVFFI2976GMOS](/sequence-files/IGVFFI2976GMOS/) 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/IGVFDS2972LLXA/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2972LLXA](/auxiliary-sets/IGVFDS2972LLXA/) has sequence file(s) [IGVFFI3079NZEG](/sequence-files/IGVFFI3079NZEG/), [IGVFFI7949SZEK](/sequence-files/IGVFFI7949SZEK/), [IGVFFI6666QLTV](/sequence-files/IGVFFI6666QLTV/), [IGVFFI8980JRKI](/sequence-files/IGVFFI8980JRKI/), [IGVFFI4337GCRP](/sequence-files/IGVFFI4337GCRP/), [IGVFFI2127ZLYL](/sequence-files/IGVFFI2127ZLYL/), [IGVFFI7754ICDD](/sequence-files/IGVFFI7754ICDD/), [IGVFFI5492LLUC](/sequence-files/IGVFFI5492LLUC/), [IGVFFI2508AAIU](/sequence-files/IGVFFI2508AAIU/), [IGVFFI4299MZIY](/sequence-files/IGVFFI4299MZIY/), [IGVFFI7025QNKP](/sequence-files/IGVFFI7025QNKP/), [IGVFFI9400RMGI](/sequence-files/IGVFFI9400RMGI/), [IGVFFI1875DXRD](/sequence-files/IGVFFI1875DXRD/), [IGVFFI3322MNRK](/sequence-files/IGVFFI3322MNRK/), [IGVFFI3780XPOL](/sequence-files/IGVFFI3780XPOL/), [IGVFFI2250TDFC](/sequence-files/IGVFFI2250TDFC/), [IGVFFI7927JOGR](/sequence-files/IGVFFI7927JOGR/), [IGVFFI7771RGUQ](/sequence-files/IGVFFI7771RGUQ/), [IGVFFI9785BXJQ](/sequence-files/IGVFFI9785BXJQ/), [IGVFFI7964MLAD](/sequence-files/IGVFFI7964MLAD/), [IGVFFI3684OAEZ](/sequence-files/IGVFFI3684OAEZ/), [IGVFFI8150MHSA](/sequence-files/IGVFFI8150MHSA/), [IGVFFI2067VNBK](/sequence-files/IGVFFI2067VNBK/), [IGVFFI3175IPAG](/sequence-files/IGVFFI3175IPAG/), [IGVFFI6653HVSW](/sequence-files/IGVFFI6653HVSW/), [IGVFFI8657NYAV](/sequence-files/IGVFFI8657NYAV/), [IGVFFI8157YIDD](/sequence-files/IGVFFI8157YIDD/), [IGVFFI5221VOBZ](/sequence-files/IGVFFI5221VOBZ/), [IGVFFI1355QYLF](/sequence-files/IGVFFI1355QYLF/), [IGVFFI1312RODU](/sequence-files/IGVFFI1312RODU/), [IGVFFI1259DZIX](/sequence-files/IGVFFI1259DZIX/), [IGVFFI5849MCSN](/sequence-files/IGVFFI5849MCSN/), [IGVFFI9204YAJH](/sequence-files/IGVFFI9204YAJH/), [IGVFFI9553HJAO](/sequence-files/IGVFFI9553HJAO/), [IGVFFI1740MSCJ](/sequence-files/IGVFFI1740MSCJ/), [IGVFFI1540YXCW](/sequence-files/IGVFFI1540YXCW/), [IGVFFI0985NIJF](/sequence-files/IGVFFI0985NIJF/), [IGVFFI0283YQAF](/sequence-files/IGVFFI0283YQAF/), [IGVFFI1095TZZN](/sequence-files/IGVFFI1095TZZN/), [IGVFFI5693ZVWI](/sequence-files/IGVFFI5693ZVWI/), [IGVFFI2572ASWX](/sequence-files/IGVFFI2572ASWX/), [IGVFFI6178SMTS](/sequence-files/IGVFFI6178SMTS/), [IGVFFI3821QRGY](/sequence-files/IGVFFI3821QRGY/), [IGVFFI3988BDGZ](/sequence-files/IGVFFI3988BDGZ/), [IGVFFI2419TMOK](/sequence-files/IGVFFI2419TMOK/), [IGVFFI7028HVED](/sequence-files/IGVFFI7028HVED/), [IGVFFI0642NPOT](/sequence-files/IGVFFI0642NPOT/), [IGVFFI2976GMOS](/sequence-files/IGVFFI2976GMOS/) 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/IGVFDS2972LLXA/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2972LLXA](/auxiliary-sets/IGVFDS2972LLXA/) 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/IGVFDS2972LLXA/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2972LLXA/",
"accession": "IGVFDS2972LLXA",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:43.586340+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/IGVFDS4359OODY/"
],
"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": "2023-12-20T23:07:28.267743+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0694FDBK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0694FDBK",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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_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 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": "2023-12-13T08:50:29.883395+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": "5ec4b318-57e8-493e-accc-7558b2e4bb5d"
}