{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6069DTLX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6069DTLX",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-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 measurement set [IGVFDS6069DTLX](/measurement-sets/IGVFDS6069DTLX/) has in progress subobject auxiliary set [IGVFDS3782ONAU](/auxiliary-sets/IGVFDS3782ONAU/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6069DTLX/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6825VUYA](/in-vitro-systems/IGVFSM6825VUYA/) 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/IGVFSM6825VUYA/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6069DTLX](/measurement-sets/IGVFDS6069DTLX/) 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/IGVFDS6069DTLX/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3782ONAU](/auxiliary-sets/IGVFDS3782ONAU/) has sequence file(s): [IGVFFI0828ALTY](/sequence-files/IGVFFI0828ALTY/), [IGVFFI7943MPFL](/sequence-files/IGVFFI7943MPFL/), [IGVFFI7511RVXS](/sequence-files/IGVFFI7511RVXS/), [IGVFFI8439EZIO](/sequence-files/IGVFFI8439EZIO/), [IGVFFI5992OWKS](/sequence-files/IGVFFI5992OWKS/), [IGVFFI6810RHTC](/sequence-files/IGVFFI6810RHTC/), [IGVFFI6367SPRA](/sequence-files/IGVFFI6367SPRA/), [IGVFFI5329OLFX](/sequence-files/IGVFFI5329OLFX/), [IGVFFI8693IRLY](/sequence-files/IGVFFI8693IRLY/), [IGVFFI7207DXFZ](/sequence-files/IGVFFI7207DXFZ/), [IGVFFI5496EIFJ](/sequence-files/IGVFFI5496EIFJ/), [IGVFFI1929PCRK](/sequence-files/IGVFFI1929PCRK/), [IGVFFI9359DXPL](/sequence-files/IGVFFI9359DXPL/), [IGVFFI2181ZDMK](/sequence-files/IGVFFI2181ZDMK/), [IGVFFI6592ZPQI](/sequence-files/IGVFFI6592ZPQI/), [IGVFFI5236KFKM](/sequence-files/IGVFFI5236KFKM/), [IGVFFI1906UNUH](/sequence-files/IGVFFI1906UNUH/), [IGVFFI4852PUDL](/sequence-files/IGVFFI4852PUDL/), [IGVFFI2532SHOQ](/sequence-files/IGVFFI2532SHOQ/), [IGVFFI6920LXUL](/sequence-files/IGVFFI6920LXUL/), [IGVFFI2174CUDH](/sequence-files/IGVFFI2174CUDH/), [IGVFFI3802PDIH](/sequence-files/IGVFFI3802PDIH/), [IGVFFI5654ANXD](/sequence-files/IGVFFI5654ANXD/), [IGVFFI2893SHME](/sequence-files/IGVFFI2893SHME/), [IGVFFI3813LKUJ](/sequence-files/IGVFFI3813LKUJ/), [IGVFFI7765PJTH](/sequence-files/IGVFFI7765PJTH/), [IGVFFI0083IQVA](/sequence-files/IGVFFI0083IQVA/), [IGVFFI5545FHMX](/sequence-files/IGVFFI5545FHMX/), [IGVFFI0635MXCO](/sequence-files/IGVFFI0635MXCO/), [IGVFFI3832QCQV](/sequence-files/IGVFFI3832QCQV/), [IGVFFI5968AEOH](/sequence-files/IGVFFI5968AEOH/), [IGVFFI7290WOAY](/sequence-files/IGVFFI7290WOAY/), [IGVFFI9573REMY](/sequence-files/IGVFFI9573REMY/), [IGVFFI1316MVQQ](/sequence-files/IGVFFI1316MVQQ/), [IGVFFI4686JXAD](/sequence-files/IGVFFI4686JXAD/), [IGVFFI7652HYRJ](/sequence-files/IGVFFI7652HYRJ/), [IGVFFI1806QDVK](/sequence-files/IGVFFI1806QDVK/), [IGVFFI6725FEQK](/sequence-files/IGVFFI6725FEQK/), [IGVFFI2154BVLZ](/sequence-files/IGVFFI2154BVLZ/), [IGVFFI7818HUVU](/sequence-files/IGVFFI7818HUVU/), [IGVFFI6284QMCF](/sequence-files/IGVFFI6284QMCF/), [IGVFFI2859CJUE](/sequence-files/IGVFFI2859CJUE/), [IGVFFI8305XOHX](/sequence-files/IGVFFI8305XOHX/), [IGVFFI0521PXKD](/sequence-files/IGVFFI0521PXKD/), [IGVFFI8620JTBW](/sequence-files/IGVFFI8620JTBW/), [IGVFFI8660JDHQ](/sequence-files/IGVFFI8660JDHQ/), [IGVFFI2344TUAX](/sequence-files/IGVFFI2344TUAX/), [IGVFFI6731UEMI](/sequence-files/IGVFFI6731UEMI/) 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/IGVFDS3782ONAU/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3782ONAU](/auxiliary-sets/IGVFDS3782ONAU/) has sequence file(s) [IGVFFI0828ALTY](/sequence-files/IGVFFI0828ALTY/), [IGVFFI7943MPFL](/sequence-files/IGVFFI7943MPFL/), [IGVFFI7511RVXS](/sequence-files/IGVFFI7511RVXS/), [IGVFFI8439EZIO](/sequence-files/IGVFFI8439EZIO/), [IGVFFI5992OWKS](/sequence-files/IGVFFI5992OWKS/), [IGVFFI6810RHTC](/sequence-files/IGVFFI6810RHTC/), [IGVFFI6367SPRA](/sequence-files/IGVFFI6367SPRA/), [IGVFFI5329OLFX](/sequence-files/IGVFFI5329OLFX/), [IGVFFI8693IRLY](/sequence-files/IGVFFI8693IRLY/), [IGVFFI7207DXFZ](/sequence-files/IGVFFI7207DXFZ/), [IGVFFI5496EIFJ](/sequence-files/IGVFFI5496EIFJ/), [IGVFFI1929PCRK](/sequence-files/IGVFFI1929PCRK/), [IGVFFI9359DXPL](/sequence-files/IGVFFI9359DXPL/), [IGVFFI2181ZDMK](/sequence-files/IGVFFI2181ZDMK/), [IGVFFI6592ZPQI](/sequence-files/IGVFFI6592ZPQI/), [IGVFFI5236KFKM](/sequence-files/IGVFFI5236KFKM/), [IGVFFI1906UNUH](/sequence-files/IGVFFI1906UNUH/), [IGVFFI4852PUDL](/sequence-files/IGVFFI4852PUDL/), [IGVFFI2532SHOQ](/sequence-files/IGVFFI2532SHOQ/), [IGVFFI6920LXUL](/sequence-files/IGVFFI6920LXUL/), [IGVFFI2174CUDH](/sequence-files/IGVFFI2174CUDH/), [IGVFFI3802PDIH](/sequence-files/IGVFFI3802PDIH/), [IGVFFI5654ANXD](/sequence-files/IGVFFI5654ANXD/), [IGVFFI2893SHME](/sequence-files/IGVFFI2893SHME/), [IGVFFI3813LKUJ](/sequence-files/IGVFFI3813LKUJ/), [IGVFFI7765PJTH](/sequence-files/IGVFFI7765PJTH/), [IGVFFI0083IQVA](/sequence-files/IGVFFI0083IQVA/), [IGVFFI5545FHMX](/sequence-files/IGVFFI5545FHMX/), [IGVFFI0635MXCO](/sequence-files/IGVFFI0635MXCO/), [IGVFFI3832QCQV](/sequence-files/IGVFFI3832QCQV/), [IGVFFI5968AEOH](/sequence-files/IGVFFI5968AEOH/), [IGVFFI7290WOAY](/sequence-files/IGVFFI7290WOAY/), [IGVFFI9573REMY](/sequence-files/IGVFFI9573REMY/), [IGVFFI1316MVQQ](/sequence-files/IGVFFI1316MVQQ/), [IGVFFI4686JXAD](/sequence-files/IGVFFI4686JXAD/), [IGVFFI7652HYRJ](/sequence-files/IGVFFI7652HYRJ/), [IGVFFI1806QDVK](/sequence-files/IGVFFI1806QDVK/), [IGVFFI6725FEQK](/sequence-files/IGVFFI6725FEQK/), [IGVFFI2154BVLZ](/sequence-files/IGVFFI2154BVLZ/), [IGVFFI7818HUVU](/sequence-files/IGVFFI7818HUVU/), [IGVFFI6284QMCF](/sequence-files/IGVFFI6284QMCF/), [IGVFFI2859CJUE](/sequence-files/IGVFFI2859CJUE/), [IGVFFI8305XOHX](/sequence-files/IGVFFI8305XOHX/), [IGVFFI0521PXKD](/sequence-files/IGVFFI0521PXKD/), [IGVFFI8620JTBW](/sequence-files/IGVFFI8620JTBW/), [IGVFFI8660JDHQ](/sequence-files/IGVFFI8660JDHQ/), [IGVFFI2344TUAX](/sequence-files/IGVFFI2344TUAX/), [IGVFFI6731UEMI](/sequence-files/IGVFFI6731UEMI/) 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/IGVFDS3782ONAU/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3782ONAU](/auxiliary-sets/IGVFDS3782ONAU/) 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/IGVFDS3782ONAU/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3782ONAU/",
"accession": "IGVFDS3782ONAU",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:42.044647+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": "2023-12-20T23:07:13.649024+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6825VUYA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6825VUYA",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinB"
],
"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 26-50% 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": "2023-12-13T08:42:10.248645+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": "0f8f7636-5235-4e67-9f40-16a135bb9201"
}