{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8163FWZM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8163FWZM",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinC_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 [IGVFDS8163FWZM](/measurement-sets/IGVFDS8163FWZM/) has in progress subobject auxiliary set [IGVFDS8384BWDF](/auxiliary-sets/IGVFDS8384BWDF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8163FWZM/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1008GZTD](/in-vitro-systems/IGVFSM1008GZTD/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM1008GZTD/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8163FWZM](/measurement-sets/IGVFDS8163FWZM/) 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/IGVFDS8163FWZM/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8384BWDF](/auxiliary-sets/IGVFDS8384BWDF/) has sequence file(s): [IGVFFI4856TGVQ](/sequence-files/IGVFFI4856TGVQ/), [IGVFFI2399KNOE](/sequence-files/IGVFFI2399KNOE/), [IGVFFI3452FLKR](/sequence-files/IGVFFI3452FLKR/), [IGVFFI6191YWEB](/sequence-files/IGVFFI6191YWEB/), [IGVFFI3676XCIB](/sequence-files/IGVFFI3676XCIB/), [IGVFFI9993XBEZ](/sequence-files/IGVFFI9993XBEZ/), [IGVFFI3989EWFI](/sequence-files/IGVFFI3989EWFI/), [IGVFFI8957LHEW](/sequence-files/IGVFFI8957LHEW/), [IGVFFI1957CRJW](/sequence-files/IGVFFI1957CRJW/), [IGVFFI5148UCXI](/sequence-files/IGVFFI5148UCXI/), [IGVFFI3450UJXU](/sequence-files/IGVFFI3450UJXU/), [IGVFFI9807JFXF](/sequence-files/IGVFFI9807JFXF/), [IGVFFI0626RBLC](/sequence-files/IGVFFI0626RBLC/), [IGVFFI4408EQHP](/sequence-files/IGVFFI4408EQHP/), [IGVFFI2587QXJO](/sequence-files/IGVFFI2587QXJO/), [IGVFFI5666BZQF](/sequence-files/IGVFFI5666BZQF/), [IGVFFI5564YQLO](/sequence-files/IGVFFI5564YQLO/), [IGVFFI6261FRXD](/sequence-files/IGVFFI6261FRXD/), [IGVFFI7790AUSA](/sequence-files/IGVFFI7790AUSA/), [IGVFFI4926HNHJ](/sequence-files/IGVFFI4926HNHJ/), [IGVFFI3664DMIN](/sequence-files/IGVFFI3664DMIN/), [IGVFFI6920QEXY](/sequence-files/IGVFFI6920QEXY/), [IGVFFI7097JLGF](/sequence-files/IGVFFI7097JLGF/), [IGVFFI9340YFAK](/sequence-files/IGVFFI9340YFAK/), [IGVFFI2658GABT](/sequence-files/IGVFFI2658GABT/), [IGVFFI9816VQPK](/sequence-files/IGVFFI9816VQPK/), [IGVFFI6520JMFT](/sequence-files/IGVFFI6520JMFT/), [IGVFFI1886HWNT](/sequence-files/IGVFFI1886HWNT/), [IGVFFI8440PEMF](/sequence-files/IGVFFI8440PEMF/), [IGVFFI4484EVHV](/sequence-files/IGVFFI4484EVHV/), [IGVFFI6657FXHG](/sequence-files/IGVFFI6657FXHG/), [IGVFFI9506QREY](/sequence-files/IGVFFI9506QREY/), [IGVFFI3781CGOD](/sequence-files/IGVFFI3781CGOD/), [IGVFFI9624XLDJ](/sequence-files/IGVFFI9624XLDJ/), [IGVFFI4302LGWZ](/sequence-files/IGVFFI4302LGWZ/), [IGVFFI1417RLZE](/sequence-files/IGVFFI1417RLZE/), [IGVFFI4811RTOH](/sequence-files/IGVFFI4811RTOH/), [IGVFFI2074NLOF](/sequence-files/IGVFFI2074NLOF/), [IGVFFI7610YZLV](/sequence-files/IGVFFI7610YZLV/), [IGVFFI1701KSKL](/sequence-files/IGVFFI1701KSKL/), [IGVFFI7607IDEX](/sequence-files/IGVFFI7607IDEX/), [IGVFFI5877FEEZ](/sequence-files/IGVFFI5877FEEZ/), [IGVFFI9614OHEW](/sequence-files/IGVFFI9614OHEW/), [IGVFFI3993ACUY](/sequence-files/IGVFFI3993ACUY/), [IGVFFI5457QSDQ](/sequence-files/IGVFFI5457QSDQ/), [IGVFFI3809SELT](/sequence-files/IGVFFI3809SELT/), [IGVFFI9168DQTX](/sequence-files/IGVFFI9168DQTX/), [IGVFFI0072VORE](/sequence-files/IGVFFI0072VORE/) 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/IGVFDS8384BWDF/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8384BWDF](/auxiliary-sets/IGVFDS8384BWDF/) has sequence file(s) [IGVFFI4856TGVQ](/sequence-files/IGVFFI4856TGVQ/), [IGVFFI2399KNOE](/sequence-files/IGVFFI2399KNOE/), [IGVFFI3452FLKR](/sequence-files/IGVFFI3452FLKR/), [IGVFFI6191YWEB](/sequence-files/IGVFFI6191YWEB/), [IGVFFI3676XCIB](/sequence-files/IGVFFI3676XCIB/), [IGVFFI9993XBEZ](/sequence-files/IGVFFI9993XBEZ/), [IGVFFI3989EWFI](/sequence-files/IGVFFI3989EWFI/), [IGVFFI8957LHEW](/sequence-files/IGVFFI8957LHEW/), [IGVFFI1957CRJW](/sequence-files/IGVFFI1957CRJW/), [IGVFFI5148UCXI](/sequence-files/IGVFFI5148UCXI/), [IGVFFI3450UJXU](/sequence-files/IGVFFI3450UJXU/), [IGVFFI9807JFXF](/sequence-files/IGVFFI9807JFXF/), [IGVFFI0626RBLC](/sequence-files/IGVFFI0626RBLC/), [IGVFFI4408EQHP](/sequence-files/IGVFFI4408EQHP/), [IGVFFI2587QXJO](/sequence-files/IGVFFI2587QXJO/), [IGVFFI5666BZQF](/sequence-files/IGVFFI5666BZQF/), [IGVFFI5564YQLO](/sequence-files/IGVFFI5564YQLO/), [IGVFFI6261FRXD](/sequence-files/IGVFFI6261FRXD/), [IGVFFI7790AUSA](/sequence-files/IGVFFI7790AUSA/), [IGVFFI4926HNHJ](/sequence-files/IGVFFI4926HNHJ/), [IGVFFI3664DMIN](/sequence-files/IGVFFI3664DMIN/), [IGVFFI6920QEXY](/sequence-files/IGVFFI6920QEXY/), [IGVFFI7097JLGF](/sequence-files/IGVFFI7097JLGF/), [IGVFFI9340YFAK](/sequence-files/IGVFFI9340YFAK/), [IGVFFI2658GABT](/sequence-files/IGVFFI2658GABT/), [IGVFFI9816VQPK](/sequence-files/IGVFFI9816VQPK/), [IGVFFI6520JMFT](/sequence-files/IGVFFI6520JMFT/), [IGVFFI1886HWNT](/sequence-files/IGVFFI1886HWNT/), [IGVFFI8440PEMF](/sequence-files/IGVFFI8440PEMF/), [IGVFFI4484EVHV](/sequence-files/IGVFFI4484EVHV/), [IGVFFI6657FXHG](/sequence-files/IGVFFI6657FXHG/), [IGVFFI9506QREY](/sequence-files/IGVFFI9506QREY/), [IGVFFI3781CGOD](/sequence-files/IGVFFI3781CGOD/), [IGVFFI9624XLDJ](/sequence-files/IGVFFI9624XLDJ/), [IGVFFI4302LGWZ](/sequence-files/IGVFFI4302LGWZ/), [IGVFFI1417RLZE](/sequence-files/IGVFFI1417RLZE/), [IGVFFI4811RTOH](/sequence-files/IGVFFI4811RTOH/), [IGVFFI2074NLOF](/sequence-files/IGVFFI2074NLOF/), [IGVFFI7610YZLV](/sequence-files/IGVFFI7610YZLV/), [IGVFFI1701KSKL](/sequence-files/IGVFFI1701KSKL/), [IGVFFI7607IDEX](/sequence-files/IGVFFI7607IDEX/), [IGVFFI5877FEEZ](/sequence-files/IGVFFI5877FEEZ/), [IGVFFI9614OHEW](/sequence-files/IGVFFI9614OHEW/), [IGVFFI3993ACUY](/sequence-files/IGVFFI3993ACUY/), [IGVFFI5457QSDQ](/sequence-files/IGVFFI5457QSDQ/), [IGVFFI3809SELT](/sequence-files/IGVFFI3809SELT/), [IGVFFI9168DQTX](/sequence-files/IGVFFI9168DQTX/), [IGVFFI0072VORE](/sequence-files/IGVFFI0072VORE/) 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/IGVFDS8384BWDF/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8384BWDF](/auxiliary-sets/IGVFDS8384BWDF/) 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/IGVFDS8384BWDF/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8384BWDF/",
"accession": "IGVFDS8384BWDF",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinC_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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:42.377066+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/IGVFDS4359OODY/"
],
"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": "2023-12-20T23:07:39.690508+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1008GZTD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1008GZTD",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"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 51-75% 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": "2023-12-13T08:42:20.296298+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": "23e7b10d-e34a-492d-9a7a-2b78216a74ef"
}