{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9880SAMJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9880SAMJ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-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 [IGVFDS9880SAMJ](/measurement-sets/IGVFDS9880SAMJ/) has in progress subobject auxiliary set [IGVFDS3877HUJV](/auxiliary-sets/IGVFDS3877HUJV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9880SAMJ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0425HXKG](/in-vitro-systems/IGVFSM0425HXKG/) 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/IGVFSM0425HXKG/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3877HUJV](/auxiliary-sets/IGVFDS3877HUJV/) has sequence file(s) [IGVFFI5237WXKT](/sequence-files/IGVFFI5237WXKT/), [IGVFFI8045DBRH](/sequence-files/IGVFFI8045DBRH/), [IGVFFI5303UWCW](/sequence-files/IGVFFI5303UWCW/), [IGVFFI4938XQQC](/sequence-files/IGVFFI4938XQQC/), [IGVFFI8971RNCP](/sequence-files/IGVFFI8971RNCP/), [IGVFFI0639DLTP](/sequence-files/IGVFFI0639DLTP/), [IGVFFI7814STZZ](/sequence-files/IGVFFI7814STZZ/), [IGVFFI5766UGKA](/sequence-files/IGVFFI5766UGKA/), [IGVFFI5341CZHN](/sequence-files/IGVFFI5341CZHN/), [IGVFFI3891XOWU](/sequence-files/IGVFFI3891XOWU/), [IGVFFI5216WORF](/sequence-files/IGVFFI5216WORF/), [IGVFFI9538UKYI](/sequence-files/IGVFFI9538UKYI/), [IGVFFI7370FGAL](/sequence-files/IGVFFI7370FGAL/), [IGVFFI6678KRCD](/sequence-files/IGVFFI6678KRCD/), [IGVFFI6185PUPQ](/sequence-files/IGVFFI6185PUPQ/), [IGVFFI8802CEYE](/sequence-files/IGVFFI8802CEYE/), [IGVFFI1837CZNX](/sequence-files/IGVFFI1837CZNX/), [IGVFFI1549SYKV](/sequence-files/IGVFFI1549SYKV/), [IGVFFI3668BISN](/sequence-files/IGVFFI3668BISN/), [IGVFFI0500TLSN](/sequence-files/IGVFFI0500TLSN/), [IGVFFI1987FBOD](/sequence-files/IGVFFI1987FBOD/), [IGVFFI3414UQDV](/sequence-files/IGVFFI3414UQDV/), [IGVFFI2255CQUA](/sequence-files/IGVFFI2255CQUA/), [IGVFFI8058JFNA](/sequence-files/IGVFFI8058JFNA/), [IGVFFI9114FXPF](/sequence-files/IGVFFI9114FXPF/), [IGVFFI7451BWUU](/sequence-files/IGVFFI7451BWUU/), [IGVFFI4142CJON](/sequence-files/IGVFFI4142CJON/), [IGVFFI1575FIKC](/sequence-files/IGVFFI1575FIKC/), [IGVFFI4077YUEX](/sequence-files/IGVFFI4077YUEX/), [IGVFFI9222FTVM](/sequence-files/IGVFFI9222FTVM/), [IGVFFI3993LSKG](/sequence-files/IGVFFI3993LSKG/), [IGVFFI2766XRSC](/sequence-files/IGVFFI2766XRSC/), [IGVFFI8924DLZG](/sequence-files/IGVFFI8924DLZG/), [IGVFFI8350ONYK](/sequence-files/IGVFFI8350ONYK/), [IGVFFI3089ONQN](/sequence-files/IGVFFI3089ONQN/), [IGVFFI3185IEQB](/sequence-files/IGVFFI3185IEQB/), [IGVFFI2196KYUA](/sequence-files/IGVFFI2196KYUA/), [IGVFFI1926BWQM](/sequence-files/IGVFFI1926BWQM/), [IGVFFI4321AQUF](/sequence-files/IGVFFI4321AQUF/), [IGVFFI8445SUJK](/sequence-files/IGVFFI8445SUJK/), [IGVFFI6907KVFS](/sequence-files/IGVFFI6907KVFS/), [IGVFFI0641VMHM](/sequence-files/IGVFFI0641VMHM/), [IGVFFI8394NWWI](/sequence-files/IGVFFI8394NWWI/), [IGVFFI3553BQUL](/sequence-files/IGVFFI3553BQUL/), [IGVFFI3360YTGE](/sequence-files/IGVFFI3360YTGE/), [IGVFFI5501FITI](/sequence-files/IGVFFI5501FITI/), [IGVFFI1042LQUB](/sequence-files/IGVFFI1042LQUB/), [IGVFFI6432BOCW](/sequence-files/IGVFFI6432BOCW/) 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/IGVFDS3877HUJV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3877HUJV](/auxiliary-sets/IGVFDS3877HUJV/) has sequence file(s): [IGVFFI5237WXKT](/sequence-files/IGVFFI5237WXKT/), [IGVFFI8045DBRH](/sequence-files/IGVFFI8045DBRH/), [IGVFFI5303UWCW](/sequence-files/IGVFFI5303UWCW/), [IGVFFI4938XQQC](/sequence-files/IGVFFI4938XQQC/), [IGVFFI8971RNCP](/sequence-files/IGVFFI8971RNCP/), [IGVFFI0639DLTP](/sequence-files/IGVFFI0639DLTP/), [IGVFFI7814STZZ](/sequence-files/IGVFFI7814STZZ/), [IGVFFI5766UGKA](/sequence-files/IGVFFI5766UGKA/), [IGVFFI5341CZHN](/sequence-files/IGVFFI5341CZHN/), [IGVFFI3891XOWU](/sequence-files/IGVFFI3891XOWU/), [IGVFFI5216WORF](/sequence-files/IGVFFI5216WORF/), [IGVFFI9538UKYI](/sequence-files/IGVFFI9538UKYI/), [IGVFFI7370FGAL](/sequence-files/IGVFFI7370FGAL/), [IGVFFI6678KRCD](/sequence-files/IGVFFI6678KRCD/), [IGVFFI6185PUPQ](/sequence-files/IGVFFI6185PUPQ/), [IGVFFI8802CEYE](/sequence-files/IGVFFI8802CEYE/), [IGVFFI1837CZNX](/sequence-files/IGVFFI1837CZNX/), [IGVFFI1549SYKV](/sequence-files/IGVFFI1549SYKV/), [IGVFFI3668BISN](/sequence-files/IGVFFI3668BISN/), [IGVFFI0500TLSN](/sequence-files/IGVFFI0500TLSN/), [IGVFFI1987FBOD](/sequence-files/IGVFFI1987FBOD/), [IGVFFI3414UQDV](/sequence-files/IGVFFI3414UQDV/), [IGVFFI2255CQUA](/sequence-files/IGVFFI2255CQUA/), [IGVFFI8058JFNA](/sequence-files/IGVFFI8058JFNA/), [IGVFFI9114FXPF](/sequence-files/IGVFFI9114FXPF/), [IGVFFI7451BWUU](/sequence-files/IGVFFI7451BWUU/), [IGVFFI4142CJON](/sequence-files/IGVFFI4142CJON/), [IGVFFI1575FIKC](/sequence-files/IGVFFI1575FIKC/), [IGVFFI4077YUEX](/sequence-files/IGVFFI4077YUEX/), [IGVFFI9222FTVM](/sequence-files/IGVFFI9222FTVM/), [IGVFFI3993LSKG](/sequence-files/IGVFFI3993LSKG/), [IGVFFI2766XRSC](/sequence-files/IGVFFI2766XRSC/), [IGVFFI8924DLZG](/sequence-files/IGVFFI8924DLZG/), [IGVFFI8350ONYK](/sequence-files/IGVFFI8350ONYK/), [IGVFFI3089ONQN](/sequence-files/IGVFFI3089ONQN/), [IGVFFI3185IEQB](/sequence-files/IGVFFI3185IEQB/), [IGVFFI2196KYUA](/sequence-files/IGVFFI2196KYUA/), [IGVFFI1926BWQM](/sequence-files/IGVFFI1926BWQM/), [IGVFFI4321AQUF](/sequence-files/IGVFFI4321AQUF/), [IGVFFI8445SUJK](/sequence-files/IGVFFI8445SUJK/), [IGVFFI6907KVFS](/sequence-files/IGVFFI6907KVFS/), [IGVFFI0641VMHM](/sequence-files/IGVFFI0641VMHM/), [IGVFFI8394NWWI](/sequence-files/IGVFFI8394NWWI/), [IGVFFI3553BQUL](/sequence-files/IGVFFI3553BQUL/), [IGVFFI3360YTGE](/sequence-files/IGVFFI3360YTGE/), [IGVFFI5501FITI](/sequence-files/IGVFFI5501FITI/), [IGVFFI1042LQUB](/sequence-files/IGVFFI1042LQUB/), [IGVFFI6432BOCW](/sequence-files/IGVFFI6432BOCW/) 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/IGVFDS3877HUJV/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9880SAMJ](/measurement-sets/IGVFDS9880SAMJ/) 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/IGVFDS9880SAMJ/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3877HUJV](/auxiliary-sets/IGVFDS3877HUJV/) 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/IGVFDS3877HUJV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3877HUJV/",
"accession": "IGVFDS3877HUJV",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-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": "2023-12-13T08:01:45.179071+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/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": "2023-12-20T23:08:06.997920+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0425HXKG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0425HXKG",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-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 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": "2023-12-13T08:58:50.439180+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": "fa80915b-6ed1-4719-95bc-30b16118a77f"
}