{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0471SKEE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0471SKEE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-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 in vitro system [IGVFSM0686AMNU](/in-vitro-systems/IGVFSM0686AMNU/) 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/IGVFSM0686AMNU/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0471SKEE](/measurement-sets/IGVFDS0471SKEE/) has in progress subobject auxiliary set [IGVFDS9497PXTX](/auxiliary-sets/IGVFDS9497PXTX/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0471SKEE/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9497PXTX](/auxiliary-sets/IGVFDS9497PXTX/) has sequence file(s) [IGVFFI5565KZVB](/sequence-files/IGVFFI5565KZVB/), [IGVFFI4541FPLW](/sequence-files/IGVFFI4541FPLW/), [IGVFFI4058DIPB](/sequence-files/IGVFFI4058DIPB/), [IGVFFI0426MGGW](/sequence-files/IGVFFI0426MGGW/), [IGVFFI9206UERB](/sequence-files/IGVFFI9206UERB/), [IGVFFI6248WPJI](/sequence-files/IGVFFI6248WPJI/), [IGVFFI1001IOJW](/sequence-files/IGVFFI1001IOJW/), [IGVFFI5823SWPQ](/sequence-files/IGVFFI5823SWPQ/), [IGVFFI7144GSYK](/sequence-files/IGVFFI7144GSYK/), [IGVFFI1641NPTH](/sequence-files/IGVFFI1641NPTH/), [IGVFFI0723VKBP](/sequence-files/IGVFFI0723VKBP/), [IGVFFI6035KFZG](/sequence-files/IGVFFI6035KFZG/), [IGVFFI6202XSEF](/sequence-files/IGVFFI6202XSEF/), [IGVFFI8262XSAD](/sequence-files/IGVFFI8262XSAD/), [IGVFFI3698KORQ](/sequence-files/IGVFFI3698KORQ/), [IGVFFI4913SZHQ](/sequence-files/IGVFFI4913SZHQ/), [IGVFFI0406OVIT](/sequence-files/IGVFFI0406OVIT/), [IGVFFI5123IYGS](/sequence-files/IGVFFI5123IYGS/), [IGVFFI5584LZNM](/sequence-files/IGVFFI5584LZNM/), [IGVFFI7372QGAR](/sequence-files/IGVFFI7372QGAR/), [IGVFFI6029RBTZ](/sequence-files/IGVFFI6029RBTZ/), [IGVFFI4260PHRM](/sequence-files/IGVFFI4260PHRM/), [IGVFFI4671ZAOX](/sequence-files/IGVFFI4671ZAOX/), [IGVFFI0593ZCPD](/sequence-files/IGVFFI0593ZCPD/), [IGVFFI7294AEVY](/sequence-files/IGVFFI7294AEVY/), [IGVFFI1389KRDV](/sequence-files/IGVFFI1389KRDV/), [IGVFFI9047LVDV](/sequence-files/IGVFFI9047LVDV/), [IGVFFI1503EILG](/sequence-files/IGVFFI1503EILG/), [IGVFFI6766WUEF](/sequence-files/IGVFFI6766WUEF/), [IGVFFI4174DYVM](/sequence-files/IGVFFI4174DYVM/), [IGVFFI4988CFLL](/sequence-files/IGVFFI4988CFLL/), [IGVFFI4516PUIP](/sequence-files/IGVFFI4516PUIP/), [IGVFFI4544OJLY](/sequence-files/IGVFFI4544OJLY/), [IGVFFI8820ZMZN](/sequence-files/IGVFFI8820ZMZN/), [IGVFFI9865TFMK](/sequence-files/IGVFFI9865TFMK/), [IGVFFI9149TGQQ](/sequence-files/IGVFFI9149TGQQ/), [IGVFFI6449RIUM](/sequence-files/IGVFFI6449RIUM/), [IGVFFI6796XXVW](/sequence-files/IGVFFI6796XXVW/), [IGVFFI7362VQLG](/sequence-files/IGVFFI7362VQLG/), [IGVFFI2752HVXD](/sequence-files/IGVFFI2752HVXD/), [IGVFFI7345TSYK](/sequence-files/IGVFFI7345TSYK/), [IGVFFI1924AZXM](/sequence-files/IGVFFI1924AZXM/), [IGVFFI0392XJRX](/sequence-files/IGVFFI0392XJRX/), [IGVFFI9251LHQV](/sequence-files/IGVFFI9251LHQV/), [IGVFFI3494RXPP](/sequence-files/IGVFFI3494RXPP/), [IGVFFI6765MFNV](/sequence-files/IGVFFI6765MFNV/), [IGVFFI2940XFHY](/sequence-files/IGVFFI2940XFHY/), [IGVFFI8735KIVA](/sequence-files/IGVFFI8735KIVA/) 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/IGVFDS9497PXTX/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9497PXTX](/auxiliary-sets/IGVFDS9497PXTX/) has sequence file(s): [IGVFFI5565KZVB](/sequence-files/IGVFFI5565KZVB/), [IGVFFI4541FPLW](/sequence-files/IGVFFI4541FPLW/), [IGVFFI4058DIPB](/sequence-files/IGVFFI4058DIPB/), [IGVFFI0426MGGW](/sequence-files/IGVFFI0426MGGW/), [IGVFFI9206UERB](/sequence-files/IGVFFI9206UERB/), [IGVFFI6248WPJI](/sequence-files/IGVFFI6248WPJI/), [IGVFFI1001IOJW](/sequence-files/IGVFFI1001IOJW/), [IGVFFI5823SWPQ](/sequence-files/IGVFFI5823SWPQ/), [IGVFFI7144GSYK](/sequence-files/IGVFFI7144GSYK/), [IGVFFI1641NPTH](/sequence-files/IGVFFI1641NPTH/), [IGVFFI0723VKBP](/sequence-files/IGVFFI0723VKBP/), [IGVFFI6035KFZG](/sequence-files/IGVFFI6035KFZG/), [IGVFFI6202XSEF](/sequence-files/IGVFFI6202XSEF/), [IGVFFI8262XSAD](/sequence-files/IGVFFI8262XSAD/), [IGVFFI3698KORQ](/sequence-files/IGVFFI3698KORQ/), [IGVFFI4913SZHQ](/sequence-files/IGVFFI4913SZHQ/), [IGVFFI0406OVIT](/sequence-files/IGVFFI0406OVIT/), [IGVFFI5123IYGS](/sequence-files/IGVFFI5123IYGS/), [IGVFFI5584LZNM](/sequence-files/IGVFFI5584LZNM/), [IGVFFI7372QGAR](/sequence-files/IGVFFI7372QGAR/), [IGVFFI6029RBTZ](/sequence-files/IGVFFI6029RBTZ/), [IGVFFI4260PHRM](/sequence-files/IGVFFI4260PHRM/), [IGVFFI4671ZAOX](/sequence-files/IGVFFI4671ZAOX/), [IGVFFI0593ZCPD](/sequence-files/IGVFFI0593ZCPD/), [IGVFFI7294AEVY](/sequence-files/IGVFFI7294AEVY/), [IGVFFI1389KRDV](/sequence-files/IGVFFI1389KRDV/), [IGVFFI9047LVDV](/sequence-files/IGVFFI9047LVDV/), [IGVFFI1503EILG](/sequence-files/IGVFFI1503EILG/), [IGVFFI6766WUEF](/sequence-files/IGVFFI6766WUEF/), [IGVFFI4174DYVM](/sequence-files/IGVFFI4174DYVM/), [IGVFFI4988CFLL](/sequence-files/IGVFFI4988CFLL/), [IGVFFI4516PUIP](/sequence-files/IGVFFI4516PUIP/), [IGVFFI4544OJLY](/sequence-files/IGVFFI4544OJLY/), [IGVFFI8820ZMZN](/sequence-files/IGVFFI8820ZMZN/), [IGVFFI9865TFMK](/sequence-files/IGVFFI9865TFMK/), [IGVFFI9149TGQQ](/sequence-files/IGVFFI9149TGQQ/), [IGVFFI6449RIUM](/sequence-files/IGVFFI6449RIUM/), [IGVFFI6796XXVW](/sequence-files/IGVFFI6796XXVW/), [IGVFFI7362VQLG](/sequence-files/IGVFFI7362VQLG/), [IGVFFI2752HVXD](/sequence-files/IGVFFI2752HVXD/), [IGVFFI7345TSYK](/sequence-files/IGVFFI7345TSYK/), [IGVFFI1924AZXM](/sequence-files/IGVFFI1924AZXM/), [IGVFFI0392XJRX](/sequence-files/IGVFFI0392XJRX/), [IGVFFI9251LHQV](/sequence-files/IGVFFI9251LHQV/), [IGVFFI3494RXPP](/sequence-files/IGVFFI3494RXPP/), [IGVFFI6765MFNV](/sequence-files/IGVFFI6765MFNV/), [IGVFFI2940XFHY](/sequence-files/IGVFFI2940XFHY/), [IGVFFI8735KIVA](/sequence-files/IGVFFI8735KIVA/) 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/IGVFDS9497PXTX/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0471SKEE](/measurement-sets/IGVFDS0471SKEE/) 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/IGVFDS0471SKEE/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9497PXTX](/auxiliary-sets/IGVFDS9497PXTX/) 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/IGVFDS9497PXTX/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9497PXTX/",
"accession": "IGVFDS9497PXTX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:21.021565+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": "2023-12-20T23:05:54.673108+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0686AMNU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0686AMNU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinB"
],
"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 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": "2023-12-05T23:00:53.699210+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": "6b3060f9-5267-4da7-b22f-d32edb551998"
}