{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7163VHFR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7163VHFR",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-BinD_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 [IGVFDS7163VHFR](/measurement-sets/IGVFDS7163VHFR/) has in progress subobject auxiliary set [IGVFDS3084ZOCV](/auxiliary-sets/IGVFDS3084ZOCV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7163VHFR/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8534PHPO](/in-vitro-systems/IGVFSM8534PHPO/) 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/IGVFSM8534PHPO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3084ZOCV](/auxiliary-sets/IGVFDS3084ZOCV/) has sequence file(s): [IGVFFI8292TRDJ](/sequence-files/IGVFFI8292TRDJ/), [IGVFFI8163LZNL](/sequence-files/IGVFFI8163LZNL/), [IGVFFI7742QOLR](/sequence-files/IGVFFI7742QOLR/), [IGVFFI2460WNXJ](/sequence-files/IGVFFI2460WNXJ/), [IGVFFI5274IPRI](/sequence-files/IGVFFI5274IPRI/), [IGVFFI8878EWVW](/sequence-files/IGVFFI8878EWVW/), [IGVFFI3293BVNE](/sequence-files/IGVFFI3293BVNE/), [IGVFFI2202IWAB](/sequence-files/IGVFFI2202IWAB/), [IGVFFI9633YUAH](/sequence-files/IGVFFI9633YUAH/), [IGVFFI4634CIEF](/sequence-files/IGVFFI4634CIEF/), [IGVFFI3329KGJC](/sequence-files/IGVFFI3329KGJC/), [IGVFFI6807MGIS](/sequence-files/IGVFFI6807MGIS/), [IGVFFI0108HIDZ](/sequence-files/IGVFFI0108HIDZ/), [IGVFFI1780KKOS](/sequence-files/IGVFFI1780KKOS/), [IGVFFI8076ZQWY](/sequence-files/IGVFFI8076ZQWY/), [IGVFFI9875MXGG](/sequence-files/IGVFFI9875MXGG/), [IGVFFI0749NNEU](/sequence-files/IGVFFI0749NNEU/), [IGVFFI7881HDXU](/sequence-files/IGVFFI7881HDXU/), [IGVFFI8900NOBX](/sequence-files/IGVFFI8900NOBX/), [IGVFFI2749KREX](/sequence-files/IGVFFI2749KREX/), [IGVFFI4636SPYA](/sequence-files/IGVFFI4636SPYA/), [IGVFFI7495CDOL](/sequence-files/IGVFFI7495CDOL/), [IGVFFI3045PEFU](/sequence-files/IGVFFI3045PEFU/), [IGVFFI8982OHCR](/sequence-files/IGVFFI8982OHCR/), [IGVFFI4702ZRCF](/sequence-files/IGVFFI4702ZRCF/), [IGVFFI5082NRLZ](/sequence-files/IGVFFI5082NRLZ/), [IGVFFI5638URJE](/sequence-files/IGVFFI5638URJE/), [IGVFFI6210ICND](/sequence-files/IGVFFI6210ICND/), [IGVFFI4330GXJW](/sequence-files/IGVFFI4330GXJW/), [IGVFFI2052JUGS](/sequence-files/IGVFFI2052JUGS/), [IGVFFI4236FZZI](/sequence-files/IGVFFI4236FZZI/), [IGVFFI7654ERMN](/sequence-files/IGVFFI7654ERMN/), [IGVFFI5539VTNZ](/sequence-files/IGVFFI5539VTNZ/), [IGVFFI1200UTGE](/sequence-files/IGVFFI1200UTGE/), [IGVFFI1524NZVU](/sequence-files/IGVFFI1524NZVU/), [IGVFFI0145AGBT](/sequence-files/IGVFFI0145AGBT/), [IGVFFI2373CBGF](/sequence-files/IGVFFI2373CBGF/), [IGVFFI5367AKQK](/sequence-files/IGVFFI5367AKQK/), [IGVFFI3807TGBU](/sequence-files/IGVFFI3807TGBU/), [IGVFFI0742VHSS](/sequence-files/IGVFFI0742VHSS/), [IGVFFI0931WHQH](/sequence-files/IGVFFI0931WHQH/), [IGVFFI4483PGZB](/sequence-files/IGVFFI4483PGZB/), [IGVFFI5983UTXX](/sequence-files/IGVFFI5983UTXX/), [IGVFFI4594DJSZ](/sequence-files/IGVFFI4594DJSZ/), [IGVFFI2074UPYM](/sequence-files/IGVFFI2074UPYM/), [IGVFFI7392YHPQ](/sequence-files/IGVFFI7392YHPQ/), [IGVFFI0663MSMB](/sequence-files/IGVFFI0663MSMB/), [IGVFFI8464HAXP](/sequence-files/IGVFFI8464HAXP/) 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/IGVFDS3084ZOCV/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7163VHFR](/measurement-sets/IGVFDS7163VHFR/) 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/IGVFDS7163VHFR/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3084ZOCV](/auxiliary-sets/IGVFDS3084ZOCV/) has sequence file(s) [IGVFFI8292TRDJ](/sequence-files/IGVFFI8292TRDJ/), [IGVFFI8163LZNL](/sequence-files/IGVFFI8163LZNL/), [IGVFFI7742QOLR](/sequence-files/IGVFFI7742QOLR/), [IGVFFI2460WNXJ](/sequence-files/IGVFFI2460WNXJ/), [IGVFFI5274IPRI](/sequence-files/IGVFFI5274IPRI/), [IGVFFI8878EWVW](/sequence-files/IGVFFI8878EWVW/), [IGVFFI3293BVNE](/sequence-files/IGVFFI3293BVNE/), [IGVFFI2202IWAB](/sequence-files/IGVFFI2202IWAB/), [IGVFFI9633YUAH](/sequence-files/IGVFFI9633YUAH/), [IGVFFI4634CIEF](/sequence-files/IGVFFI4634CIEF/), [IGVFFI3329KGJC](/sequence-files/IGVFFI3329KGJC/), [IGVFFI6807MGIS](/sequence-files/IGVFFI6807MGIS/), [IGVFFI0108HIDZ](/sequence-files/IGVFFI0108HIDZ/), [IGVFFI1780KKOS](/sequence-files/IGVFFI1780KKOS/), [IGVFFI8076ZQWY](/sequence-files/IGVFFI8076ZQWY/), [IGVFFI9875MXGG](/sequence-files/IGVFFI9875MXGG/), [IGVFFI0749NNEU](/sequence-files/IGVFFI0749NNEU/), [IGVFFI7881HDXU](/sequence-files/IGVFFI7881HDXU/), [IGVFFI8900NOBX](/sequence-files/IGVFFI8900NOBX/), [IGVFFI2749KREX](/sequence-files/IGVFFI2749KREX/), [IGVFFI4636SPYA](/sequence-files/IGVFFI4636SPYA/), [IGVFFI7495CDOL](/sequence-files/IGVFFI7495CDOL/), [IGVFFI3045PEFU](/sequence-files/IGVFFI3045PEFU/), [IGVFFI8982OHCR](/sequence-files/IGVFFI8982OHCR/), [IGVFFI4702ZRCF](/sequence-files/IGVFFI4702ZRCF/), [IGVFFI5082NRLZ](/sequence-files/IGVFFI5082NRLZ/), [IGVFFI5638URJE](/sequence-files/IGVFFI5638URJE/), [IGVFFI6210ICND](/sequence-files/IGVFFI6210ICND/), [IGVFFI4330GXJW](/sequence-files/IGVFFI4330GXJW/), [IGVFFI2052JUGS](/sequence-files/IGVFFI2052JUGS/), [IGVFFI4236FZZI](/sequence-files/IGVFFI4236FZZI/), [IGVFFI7654ERMN](/sequence-files/IGVFFI7654ERMN/), [IGVFFI5539VTNZ](/sequence-files/IGVFFI5539VTNZ/), [IGVFFI1200UTGE](/sequence-files/IGVFFI1200UTGE/), [IGVFFI1524NZVU](/sequence-files/IGVFFI1524NZVU/), [IGVFFI0145AGBT](/sequence-files/IGVFFI0145AGBT/), [IGVFFI2373CBGF](/sequence-files/IGVFFI2373CBGF/), [IGVFFI5367AKQK](/sequence-files/IGVFFI5367AKQK/), [IGVFFI3807TGBU](/sequence-files/IGVFFI3807TGBU/), [IGVFFI0742VHSS](/sequence-files/IGVFFI0742VHSS/), [IGVFFI0931WHQH](/sequence-files/IGVFFI0931WHQH/), [IGVFFI4483PGZB](/sequence-files/IGVFFI4483PGZB/), [IGVFFI5983UTXX](/sequence-files/IGVFFI5983UTXX/), [IGVFFI4594DJSZ](/sequence-files/IGVFFI4594DJSZ/), [IGVFFI2074UPYM](/sequence-files/IGVFFI2074UPYM/), [IGVFFI7392YHPQ](/sequence-files/IGVFFI7392YHPQ/), [IGVFFI0663MSMB](/sequence-files/IGVFFI0663MSMB/), [IGVFFI8464HAXP](/sequence-files/IGVFFI8464HAXP/) 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/IGVFDS3084ZOCV/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3084ZOCV](/auxiliary-sets/IGVFDS3084ZOCV/) 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/IGVFDS3084ZOCV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3084ZOCV/",
"accession": "IGVFDS3084ZOCV",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-BinD_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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:48:15.791376+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS6299IJHG/"
],
"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": "2023-12-20T23:08:31.765727+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8534PHPO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8534PHPO",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-BinD"
],
"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_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 76-100% 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": "2023-12-13T10:24:58.816683+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": "db72b3c4-daf7-4c01-ae5a-27a4a79c197f"
}