{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2972VXMB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2972VXMB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-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 [IGVFDS2972VXMB](/measurement-sets/IGVFDS2972VXMB/) has in progress subobject auxiliary set [IGVFDS8900TKOW](/auxiliary-sets/IGVFDS8900TKOW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2972VXMB/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6320VUBH](/in-vitro-systems/IGVFSM6320VUBH/) 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/IGVFSM6320VUBH/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2972VXMB](/measurement-sets/IGVFDS2972VXMB/) 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/IGVFDS2972VXMB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8900TKOW](/auxiliary-sets/IGVFDS8900TKOW/) has sequence file(s): [IGVFFI5174DPOB](/sequence-files/IGVFFI5174DPOB/), [IGVFFI4289KGCD](/sequence-files/IGVFFI4289KGCD/), [IGVFFI6421UAUH](/sequence-files/IGVFFI6421UAUH/), [IGVFFI8532LMDJ](/sequence-files/IGVFFI8532LMDJ/), [IGVFFI4821MTLB](/sequence-files/IGVFFI4821MTLB/), [IGVFFI7114TTGP](/sequence-files/IGVFFI7114TTGP/), [IGVFFI9355HVRG](/sequence-files/IGVFFI9355HVRG/), [IGVFFI1954USZO](/sequence-files/IGVFFI1954USZO/), [IGVFFI1426INMN](/sequence-files/IGVFFI1426INMN/), [IGVFFI8207KHSU](/sequence-files/IGVFFI8207KHSU/), [IGVFFI0696XKPP](/sequence-files/IGVFFI0696XKPP/), [IGVFFI8834NSTE](/sequence-files/IGVFFI8834NSTE/), [IGVFFI3750LBJX](/sequence-files/IGVFFI3750LBJX/), [IGVFFI4169IBES](/sequence-files/IGVFFI4169IBES/), [IGVFFI5625LZHW](/sequence-files/IGVFFI5625LZHW/), [IGVFFI4743ADRG](/sequence-files/IGVFFI4743ADRG/), [IGVFFI8142YLZB](/sequence-files/IGVFFI8142YLZB/), [IGVFFI8822MXQL](/sequence-files/IGVFFI8822MXQL/), [IGVFFI9612JETZ](/sequence-files/IGVFFI9612JETZ/), [IGVFFI7240OGAK](/sequence-files/IGVFFI7240OGAK/), [IGVFFI5321CIOC](/sequence-files/IGVFFI5321CIOC/), [IGVFFI5184IFFE](/sequence-files/IGVFFI5184IFFE/), [IGVFFI3028FULR](/sequence-files/IGVFFI3028FULR/), [IGVFFI0896PLHC](/sequence-files/IGVFFI0896PLHC/), [IGVFFI0902NHPR](/sequence-files/IGVFFI0902NHPR/), [IGVFFI4333GMSC](/sequence-files/IGVFFI4333GMSC/), [IGVFFI2611RSKI](/sequence-files/IGVFFI2611RSKI/), [IGVFFI0573KOVA](/sequence-files/IGVFFI0573KOVA/), [IGVFFI7317TSSA](/sequence-files/IGVFFI7317TSSA/), [IGVFFI3976KGWO](/sequence-files/IGVFFI3976KGWO/), [IGVFFI5414PUUX](/sequence-files/IGVFFI5414PUUX/), [IGVFFI0934PIPG](/sequence-files/IGVFFI0934PIPG/), [IGVFFI5563BMBP](/sequence-files/IGVFFI5563BMBP/), [IGVFFI4196SPIG](/sequence-files/IGVFFI4196SPIG/), [IGVFFI9813DPYM](/sequence-files/IGVFFI9813DPYM/), [IGVFFI6646ZJTY](/sequence-files/IGVFFI6646ZJTY/), [IGVFFI9321HGGT](/sequence-files/IGVFFI9321HGGT/), [IGVFFI4198YWFD](/sequence-files/IGVFFI4198YWFD/), [IGVFFI9868HDDX](/sequence-files/IGVFFI9868HDDX/), [IGVFFI9744TQRY](/sequence-files/IGVFFI9744TQRY/), [IGVFFI2046GKAD](/sequence-files/IGVFFI2046GKAD/), [IGVFFI2550OEAA](/sequence-files/IGVFFI2550OEAA/), [IGVFFI0003MEJV](/sequence-files/IGVFFI0003MEJV/), [IGVFFI1965TUYQ](/sequence-files/IGVFFI1965TUYQ/), [IGVFFI7688LJZS](/sequence-files/IGVFFI7688LJZS/), [IGVFFI8375OWFQ](/sequence-files/IGVFFI8375OWFQ/), [IGVFFI5516THEH](/sequence-files/IGVFFI5516THEH/), [IGVFFI2241UEVZ](/sequence-files/IGVFFI2241UEVZ/) 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/IGVFDS8900TKOW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8900TKOW](/auxiliary-sets/IGVFDS8900TKOW/) has sequence file(s) [IGVFFI5174DPOB](/sequence-files/IGVFFI5174DPOB/), [IGVFFI4289KGCD](/sequence-files/IGVFFI4289KGCD/), [IGVFFI6421UAUH](/sequence-files/IGVFFI6421UAUH/), [IGVFFI8532LMDJ](/sequence-files/IGVFFI8532LMDJ/), [IGVFFI4821MTLB](/sequence-files/IGVFFI4821MTLB/), [IGVFFI7114TTGP](/sequence-files/IGVFFI7114TTGP/), [IGVFFI9355HVRG](/sequence-files/IGVFFI9355HVRG/), [IGVFFI1954USZO](/sequence-files/IGVFFI1954USZO/), [IGVFFI1426INMN](/sequence-files/IGVFFI1426INMN/), [IGVFFI8207KHSU](/sequence-files/IGVFFI8207KHSU/), [IGVFFI0696XKPP](/sequence-files/IGVFFI0696XKPP/), [IGVFFI8834NSTE](/sequence-files/IGVFFI8834NSTE/), [IGVFFI3750LBJX](/sequence-files/IGVFFI3750LBJX/), [IGVFFI4169IBES](/sequence-files/IGVFFI4169IBES/), [IGVFFI5625LZHW](/sequence-files/IGVFFI5625LZHW/), [IGVFFI4743ADRG](/sequence-files/IGVFFI4743ADRG/), [IGVFFI8142YLZB](/sequence-files/IGVFFI8142YLZB/), [IGVFFI8822MXQL](/sequence-files/IGVFFI8822MXQL/), [IGVFFI9612JETZ](/sequence-files/IGVFFI9612JETZ/), [IGVFFI7240OGAK](/sequence-files/IGVFFI7240OGAK/), [IGVFFI5321CIOC](/sequence-files/IGVFFI5321CIOC/), [IGVFFI5184IFFE](/sequence-files/IGVFFI5184IFFE/), [IGVFFI3028FULR](/sequence-files/IGVFFI3028FULR/), [IGVFFI0896PLHC](/sequence-files/IGVFFI0896PLHC/), [IGVFFI0902NHPR](/sequence-files/IGVFFI0902NHPR/), [IGVFFI4333GMSC](/sequence-files/IGVFFI4333GMSC/), [IGVFFI2611RSKI](/sequence-files/IGVFFI2611RSKI/), [IGVFFI0573KOVA](/sequence-files/IGVFFI0573KOVA/), [IGVFFI7317TSSA](/sequence-files/IGVFFI7317TSSA/), [IGVFFI3976KGWO](/sequence-files/IGVFFI3976KGWO/), [IGVFFI5414PUUX](/sequence-files/IGVFFI5414PUUX/), [IGVFFI0934PIPG](/sequence-files/IGVFFI0934PIPG/), [IGVFFI5563BMBP](/sequence-files/IGVFFI5563BMBP/), [IGVFFI4196SPIG](/sequence-files/IGVFFI4196SPIG/), [IGVFFI9813DPYM](/sequence-files/IGVFFI9813DPYM/), [IGVFFI6646ZJTY](/sequence-files/IGVFFI6646ZJTY/), [IGVFFI9321HGGT](/sequence-files/IGVFFI9321HGGT/), [IGVFFI4198YWFD](/sequence-files/IGVFFI4198YWFD/), [IGVFFI9868HDDX](/sequence-files/IGVFFI9868HDDX/), [IGVFFI9744TQRY](/sequence-files/IGVFFI9744TQRY/), [IGVFFI2046GKAD](/sequence-files/IGVFFI2046GKAD/), [IGVFFI2550OEAA](/sequence-files/IGVFFI2550OEAA/), [IGVFFI0003MEJV](/sequence-files/IGVFFI0003MEJV/), [IGVFFI1965TUYQ](/sequence-files/IGVFFI1965TUYQ/), [IGVFFI7688LJZS](/sequence-files/IGVFFI7688LJZS/), [IGVFFI8375OWFQ](/sequence-files/IGVFFI8375OWFQ/), [IGVFFI5516THEH](/sequence-files/IGVFFI5516THEH/), [IGVFFI2241UEVZ](/sequence-files/IGVFFI2241UEVZ/) 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/IGVFDS8900TKOW/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8900TKOW](/auxiliary-sets/IGVFDS8900TKOW/) 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/IGVFDS8900TKOW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8900TKOW/",
"accession": "IGVFDS8900TKOW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:17.603441+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/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": "2023-12-20T23:05:51.743514+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6320VUBH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6320VUBH",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinD"
],
"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 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": "2023-12-05T22:44:44.527934+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": "54fe8523-2a76-454a-83a0-37468eabd6df"
}