{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1144XHLC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1144XHLC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-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 measurement set [IGVFDS1144XHLC](/measurement-sets/IGVFDS1144XHLC/) has in progress subobject auxiliary set [IGVFDS0045CAIC](/auxiliary-sets/IGVFDS0045CAIC/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1144XHLC/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0040UFBQ](/in-vitro-systems/IGVFSM0040UFBQ/) 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/IGVFSM0040UFBQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0045CAIC](/auxiliary-sets/IGVFDS0045CAIC/) has sequence file(s) [IGVFFI6092TGAB](/sequence-files/IGVFFI6092TGAB/), [IGVFFI2566PPSW](/sequence-files/IGVFFI2566PPSW/), [IGVFFI4863TVJF](/sequence-files/IGVFFI4863TVJF/), [IGVFFI1901OHTU](/sequence-files/IGVFFI1901OHTU/), [IGVFFI0893PZWD](/sequence-files/IGVFFI0893PZWD/), [IGVFFI5309OLVN](/sequence-files/IGVFFI5309OLVN/), [IGVFFI8264KXVR](/sequence-files/IGVFFI8264KXVR/), [IGVFFI9506KMBF](/sequence-files/IGVFFI9506KMBF/), [IGVFFI7004JPAK](/sequence-files/IGVFFI7004JPAK/), [IGVFFI7593JPMV](/sequence-files/IGVFFI7593JPMV/), [IGVFFI8031MIZH](/sequence-files/IGVFFI8031MIZH/), [IGVFFI8408GZVT](/sequence-files/IGVFFI8408GZVT/), [IGVFFI0524KWWN](/sequence-files/IGVFFI0524KWWN/), [IGVFFI1533MFML](/sequence-files/IGVFFI1533MFML/), [IGVFFI0627NCQH](/sequence-files/IGVFFI0627NCQH/), [IGVFFI6497EPMA](/sequence-files/IGVFFI6497EPMA/), [IGVFFI9549TEOP](/sequence-files/IGVFFI9549TEOP/), [IGVFFI3367TFSD](/sequence-files/IGVFFI3367TFSD/), [IGVFFI6480HCQM](/sequence-files/IGVFFI6480HCQM/), [IGVFFI1542BUMT](/sequence-files/IGVFFI1542BUMT/), [IGVFFI5513SFLC](/sequence-files/IGVFFI5513SFLC/), [IGVFFI0341OVOB](/sequence-files/IGVFFI0341OVOB/), [IGVFFI1219ASMM](/sequence-files/IGVFFI1219ASMM/), [IGVFFI6303BWPY](/sequence-files/IGVFFI6303BWPY/), [IGVFFI9456QPMY](/sequence-files/IGVFFI9456QPMY/), [IGVFFI3930XYCN](/sequence-files/IGVFFI3930XYCN/), [IGVFFI9319NLLE](/sequence-files/IGVFFI9319NLLE/), [IGVFFI6761RGRU](/sequence-files/IGVFFI6761RGRU/), [IGVFFI6887QKAR](/sequence-files/IGVFFI6887QKAR/), [IGVFFI2377JODR](/sequence-files/IGVFFI2377JODR/), [IGVFFI2496YDNT](/sequence-files/IGVFFI2496YDNT/), [IGVFFI0282WPLY](/sequence-files/IGVFFI0282WPLY/), [IGVFFI2157SJGP](/sequence-files/IGVFFI2157SJGP/), [IGVFFI2780RGAA](/sequence-files/IGVFFI2780RGAA/), [IGVFFI1786AGIJ](/sequence-files/IGVFFI1786AGIJ/), [IGVFFI2686JMAL](/sequence-files/IGVFFI2686JMAL/), [IGVFFI5378PFKN](/sequence-files/IGVFFI5378PFKN/), [IGVFFI7925BAKN](/sequence-files/IGVFFI7925BAKN/), [IGVFFI3090TLOC](/sequence-files/IGVFFI3090TLOC/), [IGVFFI3888GTEG](/sequence-files/IGVFFI3888GTEG/), [IGVFFI0504FXTN](/sequence-files/IGVFFI0504FXTN/), [IGVFFI4019NWEC](/sequence-files/IGVFFI4019NWEC/), [IGVFFI7522LFNA](/sequence-files/IGVFFI7522LFNA/), [IGVFFI1689LWWH](/sequence-files/IGVFFI1689LWWH/), [IGVFFI1740DFEI](/sequence-files/IGVFFI1740DFEI/), [IGVFFI5859GVCS](/sequence-files/IGVFFI5859GVCS/), [IGVFFI1128ZEUF](/sequence-files/IGVFFI1128ZEUF/), [IGVFFI6679TFJG](/sequence-files/IGVFFI6679TFJG/) 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/IGVFDS0045CAIC/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0045CAIC](/auxiliary-sets/IGVFDS0045CAIC/) has sequence file(s): [IGVFFI6092TGAB](/sequence-files/IGVFFI6092TGAB/), [IGVFFI2566PPSW](/sequence-files/IGVFFI2566PPSW/), [IGVFFI4863TVJF](/sequence-files/IGVFFI4863TVJF/), [IGVFFI1901OHTU](/sequence-files/IGVFFI1901OHTU/), [IGVFFI0893PZWD](/sequence-files/IGVFFI0893PZWD/), [IGVFFI5309OLVN](/sequence-files/IGVFFI5309OLVN/), [IGVFFI8264KXVR](/sequence-files/IGVFFI8264KXVR/), [IGVFFI9506KMBF](/sequence-files/IGVFFI9506KMBF/), [IGVFFI7004JPAK](/sequence-files/IGVFFI7004JPAK/), [IGVFFI7593JPMV](/sequence-files/IGVFFI7593JPMV/), [IGVFFI8031MIZH](/sequence-files/IGVFFI8031MIZH/), [IGVFFI8408GZVT](/sequence-files/IGVFFI8408GZVT/), [IGVFFI0524KWWN](/sequence-files/IGVFFI0524KWWN/), [IGVFFI1533MFML](/sequence-files/IGVFFI1533MFML/), [IGVFFI0627NCQH](/sequence-files/IGVFFI0627NCQH/), [IGVFFI6497EPMA](/sequence-files/IGVFFI6497EPMA/), [IGVFFI9549TEOP](/sequence-files/IGVFFI9549TEOP/), [IGVFFI3367TFSD](/sequence-files/IGVFFI3367TFSD/), [IGVFFI6480HCQM](/sequence-files/IGVFFI6480HCQM/), [IGVFFI1542BUMT](/sequence-files/IGVFFI1542BUMT/), [IGVFFI5513SFLC](/sequence-files/IGVFFI5513SFLC/), [IGVFFI0341OVOB](/sequence-files/IGVFFI0341OVOB/), [IGVFFI1219ASMM](/sequence-files/IGVFFI1219ASMM/), [IGVFFI6303BWPY](/sequence-files/IGVFFI6303BWPY/), [IGVFFI9456QPMY](/sequence-files/IGVFFI9456QPMY/), [IGVFFI3930XYCN](/sequence-files/IGVFFI3930XYCN/), [IGVFFI9319NLLE](/sequence-files/IGVFFI9319NLLE/), [IGVFFI6761RGRU](/sequence-files/IGVFFI6761RGRU/), [IGVFFI6887QKAR](/sequence-files/IGVFFI6887QKAR/), [IGVFFI2377JODR](/sequence-files/IGVFFI2377JODR/), [IGVFFI2496YDNT](/sequence-files/IGVFFI2496YDNT/), [IGVFFI0282WPLY](/sequence-files/IGVFFI0282WPLY/), [IGVFFI2157SJGP](/sequence-files/IGVFFI2157SJGP/), [IGVFFI2780RGAA](/sequence-files/IGVFFI2780RGAA/), [IGVFFI1786AGIJ](/sequence-files/IGVFFI1786AGIJ/), [IGVFFI2686JMAL](/sequence-files/IGVFFI2686JMAL/), [IGVFFI5378PFKN](/sequence-files/IGVFFI5378PFKN/), [IGVFFI7925BAKN](/sequence-files/IGVFFI7925BAKN/), [IGVFFI3090TLOC](/sequence-files/IGVFFI3090TLOC/), [IGVFFI3888GTEG](/sequence-files/IGVFFI3888GTEG/), [IGVFFI0504FXTN](/sequence-files/IGVFFI0504FXTN/), [IGVFFI4019NWEC](/sequence-files/IGVFFI4019NWEC/), [IGVFFI7522LFNA](/sequence-files/IGVFFI7522LFNA/), [IGVFFI1689LWWH](/sequence-files/IGVFFI1689LWWH/), [IGVFFI1740DFEI](/sequence-files/IGVFFI1740DFEI/), [IGVFFI5859GVCS](/sequence-files/IGVFFI5859GVCS/), [IGVFFI1128ZEUF](/sequence-files/IGVFFI1128ZEUF/), [IGVFFI6679TFJG](/sequence-files/IGVFFI6679TFJG/) 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/IGVFDS0045CAIC/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1144XHLC](/measurement-sets/IGVFDS1144XHLC/) 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/IGVFDS1144XHLC/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0045CAIC](/auxiliary-sets/IGVFDS0045CAIC/) 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/IGVFDS0045CAIC/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0045CAIC/",
"accession": "IGVFDS0045CAIC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-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": "2023-11-30T22:48:52.992399+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": "2023-12-20T23:05:41.409422+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0040UFBQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0040UFBQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-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": "2023-12-05T19:43:03.319730+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": "ca947d9f-6099-4a93-81c0-62ebe0f0ec8e"
}