{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6229XAIE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6229XAIE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-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 [IGVFDS6229XAIE](/measurement-sets/IGVFDS6229XAIE/) has in progress subobject auxiliary set [IGVFDS0059ZREO](/auxiliary-sets/IGVFDS0059ZREO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6229XAIE/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4531MGQB](/in-vitro-systems/IGVFSM4531MGQB/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM4531MGQB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0059ZREO](/auxiliary-sets/IGVFDS0059ZREO/) has sequence file(s): [IGVFFI5059CMYL](/sequence-files/IGVFFI5059CMYL/), [IGVFFI3776OETH](/sequence-files/IGVFFI3776OETH/), [IGVFFI4090BNOJ](/sequence-files/IGVFFI4090BNOJ/), [IGVFFI0376PNCG](/sequence-files/IGVFFI0376PNCG/), [IGVFFI8350CFRL](/sequence-files/IGVFFI8350CFRL/), [IGVFFI3116RVEJ](/sequence-files/IGVFFI3116RVEJ/), [IGVFFI4435WSGW](/sequence-files/IGVFFI4435WSGW/), [IGVFFI9299KLSD](/sequence-files/IGVFFI9299KLSD/), [IGVFFI3479RWOJ](/sequence-files/IGVFFI3479RWOJ/), [IGVFFI1512BVJM](/sequence-files/IGVFFI1512BVJM/), [IGVFFI4524FMUO](/sequence-files/IGVFFI4524FMUO/), [IGVFFI7001ZSGW](/sequence-files/IGVFFI7001ZSGW/), [IGVFFI7820QQKF](/sequence-files/IGVFFI7820QQKF/), [IGVFFI4062TRIW](/sequence-files/IGVFFI4062TRIW/), [IGVFFI6046CXYG](/sequence-files/IGVFFI6046CXYG/), [IGVFFI8019AHJV](/sequence-files/IGVFFI8019AHJV/), [IGVFFI7858FAFR](/sequence-files/IGVFFI7858FAFR/), [IGVFFI9057RLYV](/sequence-files/IGVFFI9057RLYV/), [IGVFFI0044EOTC](/sequence-files/IGVFFI0044EOTC/), [IGVFFI9381CLDM](/sequence-files/IGVFFI9381CLDM/), [IGVFFI8412SJLB](/sequence-files/IGVFFI8412SJLB/), [IGVFFI4400SYLA](/sequence-files/IGVFFI4400SYLA/), [IGVFFI8742XZMS](/sequence-files/IGVFFI8742XZMS/), [IGVFFI7169XBPT](/sequence-files/IGVFFI7169XBPT/), [IGVFFI2659CLIV](/sequence-files/IGVFFI2659CLIV/), [IGVFFI8297FSCV](/sequence-files/IGVFFI8297FSCV/), [IGVFFI1769PEBG](/sequence-files/IGVFFI1769PEBG/), [IGVFFI7965DZAR](/sequence-files/IGVFFI7965DZAR/), [IGVFFI7994WOJP](/sequence-files/IGVFFI7994WOJP/), [IGVFFI4791FDRT](/sequence-files/IGVFFI4791FDRT/), [IGVFFI3477YLIL](/sequence-files/IGVFFI3477YLIL/), [IGVFFI8766DIAX](/sequence-files/IGVFFI8766DIAX/), [IGVFFI4576ZNQG](/sequence-files/IGVFFI4576ZNQG/), [IGVFFI1167ZBML](/sequence-files/IGVFFI1167ZBML/), [IGVFFI6019UQGM](/sequence-files/IGVFFI6019UQGM/), [IGVFFI5393QXVF](/sequence-files/IGVFFI5393QXVF/), [IGVFFI4031DZHH](/sequence-files/IGVFFI4031DZHH/), [IGVFFI2127QDRI](/sequence-files/IGVFFI2127QDRI/), [IGVFFI8975BQEH](/sequence-files/IGVFFI8975BQEH/), [IGVFFI0982GCGH](/sequence-files/IGVFFI0982GCGH/), [IGVFFI4961UAJO](/sequence-files/IGVFFI4961UAJO/), [IGVFFI8574QCYC](/sequence-files/IGVFFI8574QCYC/), [IGVFFI6713KAIK](/sequence-files/IGVFFI6713KAIK/), [IGVFFI9113EZBH](/sequence-files/IGVFFI9113EZBH/), [IGVFFI8327LIPV](/sequence-files/IGVFFI8327LIPV/), [IGVFFI9662CGMB](/sequence-files/IGVFFI9662CGMB/), [IGVFFI1900ECUC](/sequence-files/IGVFFI1900ECUC/), [IGVFFI7136CDLT](/sequence-files/IGVFFI7136CDLT/) 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/IGVFDS0059ZREO/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6229XAIE](/measurement-sets/IGVFDS6229XAIE/) 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/IGVFDS6229XAIE/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0059ZREO](/auxiliary-sets/IGVFDS0059ZREO/) has sequence file(s) [IGVFFI5059CMYL](/sequence-files/IGVFFI5059CMYL/), [IGVFFI3776OETH](/sequence-files/IGVFFI3776OETH/), [IGVFFI4090BNOJ](/sequence-files/IGVFFI4090BNOJ/), [IGVFFI0376PNCG](/sequence-files/IGVFFI0376PNCG/), [IGVFFI8350CFRL](/sequence-files/IGVFFI8350CFRL/), [IGVFFI3116RVEJ](/sequence-files/IGVFFI3116RVEJ/), [IGVFFI4435WSGW](/sequence-files/IGVFFI4435WSGW/), [IGVFFI9299KLSD](/sequence-files/IGVFFI9299KLSD/), [IGVFFI3479RWOJ](/sequence-files/IGVFFI3479RWOJ/), [IGVFFI1512BVJM](/sequence-files/IGVFFI1512BVJM/), [IGVFFI4524FMUO](/sequence-files/IGVFFI4524FMUO/), [IGVFFI7001ZSGW](/sequence-files/IGVFFI7001ZSGW/), [IGVFFI7820QQKF](/sequence-files/IGVFFI7820QQKF/), [IGVFFI4062TRIW](/sequence-files/IGVFFI4062TRIW/), [IGVFFI6046CXYG](/sequence-files/IGVFFI6046CXYG/), [IGVFFI8019AHJV](/sequence-files/IGVFFI8019AHJV/), [IGVFFI7858FAFR](/sequence-files/IGVFFI7858FAFR/), [IGVFFI9057RLYV](/sequence-files/IGVFFI9057RLYV/), [IGVFFI0044EOTC](/sequence-files/IGVFFI0044EOTC/), [IGVFFI9381CLDM](/sequence-files/IGVFFI9381CLDM/), [IGVFFI8412SJLB](/sequence-files/IGVFFI8412SJLB/), [IGVFFI4400SYLA](/sequence-files/IGVFFI4400SYLA/), [IGVFFI8742XZMS](/sequence-files/IGVFFI8742XZMS/), [IGVFFI7169XBPT](/sequence-files/IGVFFI7169XBPT/), [IGVFFI2659CLIV](/sequence-files/IGVFFI2659CLIV/), [IGVFFI8297FSCV](/sequence-files/IGVFFI8297FSCV/), [IGVFFI1769PEBG](/sequence-files/IGVFFI1769PEBG/), [IGVFFI7965DZAR](/sequence-files/IGVFFI7965DZAR/), [IGVFFI7994WOJP](/sequence-files/IGVFFI7994WOJP/), [IGVFFI4791FDRT](/sequence-files/IGVFFI4791FDRT/), [IGVFFI3477YLIL](/sequence-files/IGVFFI3477YLIL/), [IGVFFI8766DIAX](/sequence-files/IGVFFI8766DIAX/), [IGVFFI4576ZNQG](/sequence-files/IGVFFI4576ZNQG/), [IGVFFI1167ZBML](/sequence-files/IGVFFI1167ZBML/), [IGVFFI6019UQGM](/sequence-files/IGVFFI6019UQGM/), [IGVFFI5393QXVF](/sequence-files/IGVFFI5393QXVF/), [IGVFFI4031DZHH](/sequence-files/IGVFFI4031DZHH/), [IGVFFI2127QDRI](/sequence-files/IGVFFI2127QDRI/), [IGVFFI8975BQEH](/sequence-files/IGVFFI8975BQEH/), [IGVFFI0982GCGH](/sequence-files/IGVFFI0982GCGH/), [IGVFFI4961UAJO](/sequence-files/IGVFFI4961UAJO/), [IGVFFI8574QCYC](/sequence-files/IGVFFI8574QCYC/), [IGVFFI6713KAIK](/sequence-files/IGVFFI6713KAIK/), [IGVFFI9113EZBH](/sequence-files/IGVFFI9113EZBH/), [IGVFFI8327LIPV](/sequence-files/IGVFFI8327LIPV/), [IGVFFI9662CGMB](/sequence-files/IGVFFI9662CGMB/), [IGVFFI1900ECUC](/sequence-files/IGVFFI1900ECUC/), [IGVFFI7136CDLT](/sequence-files/IGVFFI7136CDLT/) 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/IGVFDS0059ZREO/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0059ZREO](/auxiliary-sets/IGVFDS0059ZREO/) 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/IGVFDS0059ZREO/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0059ZREO/",
"accession": "IGVFDS0059ZREO",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:23.389043+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/IGVFDS5031MNRR/"
],
"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": "2023-12-20T23:05:15.846139+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4531MGQB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4531MGQB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"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": "2023-12-05T23:15:52.279206+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": "243c1919-ded6-41ae-ae6c-d039f44b0633"
}