{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3368XILR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3368XILR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinA_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 in vitro system [IGVFSM5143PODP](/in-vitro-systems/IGVFSM5143PODP/) 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/IGVFSM5143PODP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3368XILR](/measurement-sets/IGVFDS3368XILR/) has in progress subobject auxiliary set [IGVFDS1652CUMB](/auxiliary-sets/IGVFDS1652CUMB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3368XILR/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3368XILR](/measurement-sets/IGVFDS3368XILR/) 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/IGVFDS3368XILR/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1652CUMB](/auxiliary-sets/IGVFDS1652CUMB/) has sequence file(s) [IGVFFI6679CRME](/sequence-files/IGVFFI6679CRME/), [IGVFFI3569SSEU](/sequence-files/IGVFFI3569SSEU/), [IGVFFI5818JSTT](/sequence-files/IGVFFI5818JSTT/), [IGVFFI5010AKAO](/sequence-files/IGVFFI5010AKAO/), [IGVFFI3038VQZY](/sequence-files/IGVFFI3038VQZY/), [IGVFFI1687JJAX](/sequence-files/IGVFFI1687JJAX/), [IGVFFI8007IEPP](/sequence-files/IGVFFI8007IEPP/), [IGVFFI3762CZZM](/sequence-files/IGVFFI3762CZZM/), [IGVFFI4928ARVA](/sequence-files/IGVFFI4928ARVA/), [IGVFFI1844XLRC](/sequence-files/IGVFFI1844XLRC/), [IGVFFI5479XJZA](/sequence-files/IGVFFI5479XJZA/), [IGVFFI0771ANRL](/sequence-files/IGVFFI0771ANRL/), [IGVFFI4825KBEL](/sequence-files/IGVFFI4825KBEL/), [IGVFFI4152IZVG](/sequence-files/IGVFFI4152IZVG/), [IGVFFI9342MINO](/sequence-files/IGVFFI9342MINO/), [IGVFFI8269VQNH](/sequence-files/IGVFFI8269VQNH/), [IGVFFI2546JRGC](/sequence-files/IGVFFI2546JRGC/), [IGVFFI7763RAMU](/sequence-files/IGVFFI7763RAMU/), [IGVFFI8926TEGQ](/sequence-files/IGVFFI8926TEGQ/), [IGVFFI1846DCNK](/sequence-files/IGVFFI1846DCNK/), [IGVFFI2198EAKL](/sequence-files/IGVFFI2198EAKL/), [IGVFFI2741ANZC](/sequence-files/IGVFFI2741ANZC/), [IGVFFI3703OBMS](/sequence-files/IGVFFI3703OBMS/), [IGVFFI1252PONQ](/sequence-files/IGVFFI1252PONQ/), [IGVFFI4873GQTG](/sequence-files/IGVFFI4873GQTG/), [IGVFFI8840LDKR](/sequence-files/IGVFFI8840LDKR/), [IGVFFI9987UKVY](/sequence-files/IGVFFI9987UKVY/), [IGVFFI0853AZBE](/sequence-files/IGVFFI0853AZBE/), [IGVFFI5730NAZO](/sequence-files/IGVFFI5730NAZO/), [IGVFFI3420WJAY](/sequence-files/IGVFFI3420WJAY/), [IGVFFI5602KLDL](/sequence-files/IGVFFI5602KLDL/), [IGVFFI0484JFAZ](/sequence-files/IGVFFI0484JFAZ/), [IGVFFI6139OLGM](/sequence-files/IGVFFI6139OLGM/), [IGVFFI2804OVCJ](/sequence-files/IGVFFI2804OVCJ/), [IGVFFI6095EDXF](/sequence-files/IGVFFI6095EDXF/), [IGVFFI7853YVXW](/sequence-files/IGVFFI7853YVXW/), [IGVFFI1191ARLX](/sequence-files/IGVFFI1191ARLX/), [IGVFFI6280HGKG](/sequence-files/IGVFFI6280HGKG/), [IGVFFI2980OADM](/sequence-files/IGVFFI2980OADM/), [IGVFFI9692LJMU](/sequence-files/IGVFFI9692LJMU/), [IGVFFI3609LXNN](/sequence-files/IGVFFI3609LXNN/), [IGVFFI1314FRFI](/sequence-files/IGVFFI1314FRFI/), [IGVFFI8058QQFV](/sequence-files/IGVFFI8058QQFV/), [IGVFFI0829BVPD](/sequence-files/IGVFFI0829BVPD/), [IGVFFI7445HLQR](/sequence-files/IGVFFI7445HLQR/), [IGVFFI4925NZUI](/sequence-files/IGVFFI4925NZUI/), [IGVFFI5156OSFO](/sequence-files/IGVFFI5156OSFO/), [IGVFFI0685NWUQ](/sequence-files/IGVFFI0685NWUQ/) 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/IGVFDS1652CUMB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1652CUMB](/auxiliary-sets/IGVFDS1652CUMB/) has sequence file(s): [IGVFFI6679CRME](/sequence-files/IGVFFI6679CRME/), [IGVFFI3569SSEU](/sequence-files/IGVFFI3569SSEU/), [IGVFFI5818JSTT](/sequence-files/IGVFFI5818JSTT/), [IGVFFI5010AKAO](/sequence-files/IGVFFI5010AKAO/), [IGVFFI3038VQZY](/sequence-files/IGVFFI3038VQZY/), [IGVFFI1687JJAX](/sequence-files/IGVFFI1687JJAX/), [IGVFFI8007IEPP](/sequence-files/IGVFFI8007IEPP/), [IGVFFI3762CZZM](/sequence-files/IGVFFI3762CZZM/), [IGVFFI4928ARVA](/sequence-files/IGVFFI4928ARVA/), [IGVFFI1844XLRC](/sequence-files/IGVFFI1844XLRC/), [IGVFFI5479XJZA](/sequence-files/IGVFFI5479XJZA/), [IGVFFI0771ANRL](/sequence-files/IGVFFI0771ANRL/), [IGVFFI4825KBEL](/sequence-files/IGVFFI4825KBEL/), [IGVFFI4152IZVG](/sequence-files/IGVFFI4152IZVG/), [IGVFFI9342MINO](/sequence-files/IGVFFI9342MINO/), [IGVFFI8269VQNH](/sequence-files/IGVFFI8269VQNH/), [IGVFFI2546JRGC](/sequence-files/IGVFFI2546JRGC/), [IGVFFI7763RAMU](/sequence-files/IGVFFI7763RAMU/), [IGVFFI8926TEGQ](/sequence-files/IGVFFI8926TEGQ/), [IGVFFI1846DCNK](/sequence-files/IGVFFI1846DCNK/), [IGVFFI2198EAKL](/sequence-files/IGVFFI2198EAKL/), [IGVFFI2741ANZC](/sequence-files/IGVFFI2741ANZC/), [IGVFFI3703OBMS](/sequence-files/IGVFFI3703OBMS/), [IGVFFI1252PONQ](/sequence-files/IGVFFI1252PONQ/), [IGVFFI4873GQTG](/sequence-files/IGVFFI4873GQTG/), [IGVFFI8840LDKR](/sequence-files/IGVFFI8840LDKR/), [IGVFFI9987UKVY](/sequence-files/IGVFFI9987UKVY/), [IGVFFI0853AZBE](/sequence-files/IGVFFI0853AZBE/), [IGVFFI5730NAZO](/sequence-files/IGVFFI5730NAZO/), [IGVFFI3420WJAY](/sequence-files/IGVFFI3420WJAY/), [IGVFFI5602KLDL](/sequence-files/IGVFFI5602KLDL/), [IGVFFI0484JFAZ](/sequence-files/IGVFFI0484JFAZ/), [IGVFFI6139OLGM](/sequence-files/IGVFFI6139OLGM/), [IGVFFI2804OVCJ](/sequence-files/IGVFFI2804OVCJ/), [IGVFFI6095EDXF](/sequence-files/IGVFFI6095EDXF/), [IGVFFI7853YVXW](/sequence-files/IGVFFI7853YVXW/), [IGVFFI1191ARLX](/sequence-files/IGVFFI1191ARLX/), [IGVFFI6280HGKG](/sequence-files/IGVFFI6280HGKG/), [IGVFFI2980OADM](/sequence-files/IGVFFI2980OADM/), [IGVFFI9692LJMU](/sequence-files/IGVFFI9692LJMU/), [IGVFFI3609LXNN](/sequence-files/IGVFFI3609LXNN/), [IGVFFI1314FRFI](/sequence-files/IGVFFI1314FRFI/), [IGVFFI8058QQFV](/sequence-files/IGVFFI8058QQFV/), [IGVFFI0829BVPD](/sequence-files/IGVFFI0829BVPD/), [IGVFFI7445HLQR](/sequence-files/IGVFFI7445HLQR/), [IGVFFI4925NZUI](/sequence-files/IGVFFI4925NZUI/), [IGVFFI5156OSFO](/sequence-files/IGVFFI5156OSFO/), [IGVFFI0685NWUQ](/sequence-files/IGVFFI0685NWUQ/) 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/IGVFDS1652CUMB/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1652CUMB](/auxiliary-sets/IGVFDS1652CUMB/) 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/IGVFDS1652CUMB/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1652CUMB/",
"accession": "IGVFDS1652CUMB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinA_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": "2023-11-30T22:49:02.616605+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/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": "2023-12-20T23:06:01.623815+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5143PODP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5143PODP",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinA"
],
"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 0-25% 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": "2023-12-05T20:45:27.269201+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": "39070c10-197c-4ece-81fd-4dd6d53f5af5"
}