{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7009ITAD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7009ITAD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-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 in vitro system [IGVFSM6259GNEC](/in-vitro-systems/IGVFSM6259GNEC/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6259GNEC/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS7009ITAD](/measurement-sets/IGVFDS7009ITAD/) has in progress subobject auxiliary set [IGVFDS3481YJTS](/auxiliary-sets/IGVFDS3481YJTS/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7009ITAD/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3481YJTS](/auxiliary-sets/IGVFDS3481YJTS/) has sequence file(s) [IGVFFI6500PNHB](/sequence-files/IGVFFI6500PNHB/), [IGVFFI5127LIBU](/sequence-files/IGVFFI5127LIBU/), [IGVFFI5420BKIH](/sequence-files/IGVFFI5420BKIH/), [IGVFFI3386QWDP](/sequence-files/IGVFFI3386QWDP/), [IGVFFI2577RHWX](/sequence-files/IGVFFI2577RHWX/), [IGVFFI8756MZBS](/sequence-files/IGVFFI8756MZBS/), [IGVFFI2030NNQS](/sequence-files/IGVFFI2030NNQS/), [IGVFFI2069SDFI](/sequence-files/IGVFFI2069SDFI/), [IGVFFI2053LDLS](/sequence-files/IGVFFI2053LDLS/), [IGVFFI0364LFKW](/sequence-files/IGVFFI0364LFKW/), [IGVFFI6333QPRB](/sequence-files/IGVFFI6333QPRB/), [IGVFFI0076LJCM](/sequence-files/IGVFFI0076LJCM/), [IGVFFI4255BOQT](/sequence-files/IGVFFI4255BOQT/), [IGVFFI9264WGJU](/sequence-files/IGVFFI9264WGJU/), [IGVFFI9351KNCA](/sequence-files/IGVFFI9351KNCA/), [IGVFFI0907ZWJA](/sequence-files/IGVFFI0907ZWJA/), [IGVFFI4087ETZU](/sequence-files/IGVFFI4087ETZU/), [IGVFFI8442HSTB](/sequence-files/IGVFFI8442HSTB/), [IGVFFI4412DUVM](/sequence-files/IGVFFI4412DUVM/), [IGVFFI6887FGIT](/sequence-files/IGVFFI6887FGIT/), [IGVFFI3347KXEY](/sequence-files/IGVFFI3347KXEY/), [IGVFFI7741FPFD](/sequence-files/IGVFFI7741FPFD/), [IGVFFI7755FBJT](/sequence-files/IGVFFI7755FBJT/), [IGVFFI3264AYEC](/sequence-files/IGVFFI3264AYEC/), [IGVFFI5684RBSI](/sequence-files/IGVFFI5684RBSI/), [IGVFFI6450YVDW](/sequence-files/IGVFFI6450YVDW/), [IGVFFI1734UVGN](/sequence-files/IGVFFI1734UVGN/), [IGVFFI6612UUQX](/sequence-files/IGVFFI6612UUQX/), [IGVFFI6654QBXZ](/sequence-files/IGVFFI6654QBXZ/), [IGVFFI3974SGHM](/sequence-files/IGVFFI3974SGHM/), [IGVFFI5704YKDN](/sequence-files/IGVFFI5704YKDN/), [IGVFFI6996RKXA](/sequence-files/IGVFFI6996RKXA/), [IGVFFI4464KQXE](/sequence-files/IGVFFI4464KQXE/), [IGVFFI3577PBXF](/sequence-files/IGVFFI3577PBXF/), [IGVFFI7220VRID](/sequence-files/IGVFFI7220VRID/), [IGVFFI7403XIFD](/sequence-files/IGVFFI7403XIFD/), [IGVFFI8939NFZP](/sequence-files/IGVFFI8939NFZP/), [IGVFFI6877SHQZ](/sequence-files/IGVFFI6877SHQZ/), [IGVFFI9073XHJX](/sequence-files/IGVFFI9073XHJX/), [IGVFFI7535LUPR](/sequence-files/IGVFFI7535LUPR/), [IGVFFI3884VSEE](/sequence-files/IGVFFI3884VSEE/), [IGVFFI8329JUDP](/sequence-files/IGVFFI8329JUDP/), [IGVFFI5732LFOM](/sequence-files/IGVFFI5732LFOM/), [IGVFFI6586LZKE](/sequence-files/IGVFFI6586LZKE/), [IGVFFI0883TTOY](/sequence-files/IGVFFI0883TTOY/), [IGVFFI5303CSNX](/sequence-files/IGVFFI5303CSNX/), [IGVFFI8573PPSH](/sequence-files/IGVFFI8573PPSH/), [IGVFFI1460FTAQ](/sequence-files/IGVFFI1460FTAQ/) 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/IGVFDS3481YJTS/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3481YJTS](/auxiliary-sets/IGVFDS3481YJTS/) has sequence file(s): [IGVFFI6500PNHB](/sequence-files/IGVFFI6500PNHB/), [IGVFFI5127LIBU](/sequence-files/IGVFFI5127LIBU/), [IGVFFI5420BKIH](/sequence-files/IGVFFI5420BKIH/), [IGVFFI3386QWDP](/sequence-files/IGVFFI3386QWDP/), [IGVFFI2577RHWX](/sequence-files/IGVFFI2577RHWX/), [IGVFFI8756MZBS](/sequence-files/IGVFFI8756MZBS/), [IGVFFI2030NNQS](/sequence-files/IGVFFI2030NNQS/), [IGVFFI2069SDFI](/sequence-files/IGVFFI2069SDFI/), [IGVFFI2053LDLS](/sequence-files/IGVFFI2053LDLS/), [IGVFFI0364LFKW](/sequence-files/IGVFFI0364LFKW/), [IGVFFI6333QPRB](/sequence-files/IGVFFI6333QPRB/), [IGVFFI0076LJCM](/sequence-files/IGVFFI0076LJCM/), [IGVFFI4255BOQT](/sequence-files/IGVFFI4255BOQT/), [IGVFFI9264WGJU](/sequence-files/IGVFFI9264WGJU/), [IGVFFI9351KNCA](/sequence-files/IGVFFI9351KNCA/), [IGVFFI0907ZWJA](/sequence-files/IGVFFI0907ZWJA/), [IGVFFI4087ETZU](/sequence-files/IGVFFI4087ETZU/), [IGVFFI8442HSTB](/sequence-files/IGVFFI8442HSTB/), [IGVFFI4412DUVM](/sequence-files/IGVFFI4412DUVM/), [IGVFFI6887FGIT](/sequence-files/IGVFFI6887FGIT/), [IGVFFI3347KXEY](/sequence-files/IGVFFI3347KXEY/), [IGVFFI7741FPFD](/sequence-files/IGVFFI7741FPFD/), [IGVFFI7755FBJT](/sequence-files/IGVFFI7755FBJT/), [IGVFFI3264AYEC](/sequence-files/IGVFFI3264AYEC/), [IGVFFI5684RBSI](/sequence-files/IGVFFI5684RBSI/), [IGVFFI6450YVDW](/sequence-files/IGVFFI6450YVDW/), [IGVFFI1734UVGN](/sequence-files/IGVFFI1734UVGN/), [IGVFFI6612UUQX](/sequence-files/IGVFFI6612UUQX/), [IGVFFI6654QBXZ](/sequence-files/IGVFFI6654QBXZ/), [IGVFFI3974SGHM](/sequence-files/IGVFFI3974SGHM/), [IGVFFI5704YKDN](/sequence-files/IGVFFI5704YKDN/), [IGVFFI6996RKXA](/sequence-files/IGVFFI6996RKXA/), [IGVFFI4464KQXE](/sequence-files/IGVFFI4464KQXE/), [IGVFFI3577PBXF](/sequence-files/IGVFFI3577PBXF/), [IGVFFI7220VRID](/sequence-files/IGVFFI7220VRID/), [IGVFFI7403XIFD](/sequence-files/IGVFFI7403XIFD/), [IGVFFI8939NFZP](/sequence-files/IGVFFI8939NFZP/), [IGVFFI6877SHQZ](/sequence-files/IGVFFI6877SHQZ/), [IGVFFI9073XHJX](/sequence-files/IGVFFI9073XHJX/), [IGVFFI7535LUPR](/sequence-files/IGVFFI7535LUPR/), [IGVFFI3884VSEE](/sequence-files/IGVFFI3884VSEE/), [IGVFFI8329JUDP](/sequence-files/IGVFFI8329JUDP/), [IGVFFI5732LFOM](/sequence-files/IGVFFI5732LFOM/), [IGVFFI6586LZKE](/sequence-files/IGVFFI6586LZKE/), [IGVFFI0883TTOY](/sequence-files/IGVFFI0883TTOY/), [IGVFFI5303CSNX](/sequence-files/IGVFFI5303CSNX/), [IGVFFI8573PPSH](/sequence-files/IGVFFI8573PPSH/), [IGVFFI1460FTAQ](/sequence-files/IGVFFI1460FTAQ/) 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/IGVFDS3481YJTS/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7009ITAD](/measurement-sets/IGVFDS7009ITAD/) 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/IGVFDS7009ITAD/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3481YJTS](/auxiliary-sets/IGVFDS3481YJTS/) 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/IGVFDS3481YJTS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3481YJTS/",
"accession": "IGVFDS3481YJTS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:56.738309+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/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:29.421128+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6259GNEC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6259GNEC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinA"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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": "2023-12-05T22:01:34.389814+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": "3a7a8282-3a92-4f42-877e-a64086b57213"
}