{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6957VHOD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6957VHOD",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-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 [IGVFDS6957VHOD](/measurement-sets/IGVFDS6957VHOD/) has in progress subobject auxiliary set [IGVFDS1724AFUA](/auxiliary-sets/IGVFDS1724AFUA/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6957VHOD/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0117NVHQ](/in-vitro-systems/IGVFSM0117NVHQ/) 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/IGVFSM0117NVHQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1724AFUA](/auxiliary-sets/IGVFDS1724AFUA/) has sequence file(s): [IGVFFI2444NJIP](/sequence-files/IGVFFI2444NJIP/), [IGVFFI4050YOMW](/sequence-files/IGVFFI4050YOMW/), [IGVFFI3375VGEE](/sequence-files/IGVFFI3375VGEE/), [IGVFFI1824RNBS](/sequence-files/IGVFFI1824RNBS/), [IGVFFI1978DGKV](/sequence-files/IGVFFI1978DGKV/), [IGVFFI3221NMVG](/sequence-files/IGVFFI3221NMVG/), [IGVFFI2337HHXE](/sequence-files/IGVFFI2337HHXE/), [IGVFFI4468XYIH](/sequence-files/IGVFFI4468XYIH/), [IGVFFI7236MQBV](/sequence-files/IGVFFI7236MQBV/), [IGVFFI4228LZQG](/sequence-files/IGVFFI4228LZQG/), [IGVFFI4676ZZKO](/sequence-files/IGVFFI4676ZZKO/), [IGVFFI2508CVAU](/sequence-files/IGVFFI2508CVAU/), [IGVFFI2552EWQU](/sequence-files/IGVFFI2552EWQU/), [IGVFFI1357UWRB](/sequence-files/IGVFFI1357UWRB/), [IGVFFI4280RKOM](/sequence-files/IGVFFI4280RKOM/), [IGVFFI3562LFUJ](/sequence-files/IGVFFI3562LFUJ/), [IGVFFI8582LYOD](/sequence-files/IGVFFI8582LYOD/), [IGVFFI1630WZPN](/sequence-files/IGVFFI1630WZPN/), [IGVFFI9872QHGT](/sequence-files/IGVFFI9872QHGT/), [IGVFFI3686AJOK](/sequence-files/IGVFFI3686AJOK/), [IGVFFI2598FZSR](/sequence-files/IGVFFI2598FZSR/), [IGVFFI1007KHIA](/sequence-files/IGVFFI1007KHIA/), [IGVFFI4491KVYP](/sequence-files/IGVFFI4491KVYP/), [IGVFFI6870BLBA](/sequence-files/IGVFFI6870BLBA/), [IGVFFI6352FEST](/sequence-files/IGVFFI6352FEST/), [IGVFFI5218YSSQ](/sequence-files/IGVFFI5218YSSQ/), [IGVFFI7693ODNK](/sequence-files/IGVFFI7693ODNK/), [IGVFFI0849BHOW](/sequence-files/IGVFFI0849BHOW/), [IGVFFI9528LDBC](/sequence-files/IGVFFI9528LDBC/), [IGVFFI2298YXII](/sequence-files/IGVFFI2298YXII/), [IGVFFI9965SKXL](/sequence-files/IGVFFI9965SKXL/), [IGVFFI8723DKVY](/sequence-files/IGVFFI8723DKVY/), [IGVFFI5721NHIP](/sequence-files/IGVFFI5721NHIP/), [IGVFFI7200CQUK](/sequence-files/IGVFFI7200CQUK/), [IGVFFI7133XROH](/sequence-files/IGVFFI7133XROH/), [IGVFFI3045JKYB](/sequence-files/IGVFFI3045JKYB/), [IGVFFI8160SYSC](/sequence-files/IGVFFI8160SYSC/), [IGVFFI0324MEUA](/sequence-files/IGVFFI0324MEUA/), [IGVFFI3142HFGI](/sequence-files/IGVFFI3142HFGI/), [IGVFFI5783KATD](/sequence-files/IGVFFI5783KATD/), [IGVFFI3249ULJY](/sequence-files/IGVFFI3249ULJY/), [IGVFFI7019TDJB](/sequence-files/IGVFFI7019TDJB/), [IGVFFI8101TNOW](/sequence-files/IGVFFI8101TNOW/), [IGVFFI7649FEIT](/sequence-files/IGVFFI7649FEIT/), [IGVFFI8911GKWO](/sequence-files/IGVFFI8911GKWO/), [IGVFFI9957DTEQ](/sequence-files/IGVFFI9957DTEQ/), [IGVFFI0183CMJH](/sequence-files/IGVFFI0183CMJH/), [IGVFFI0708ZDVL](/sequence-files/IGVFFI0708ZDVL/) 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/IGVFDS1724AFUA/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6957VHOD](/measurement-sets/IGVFDS6957VHOD/) 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/IGVFDS6957VHOD/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1724AFUA](/auxiliary-sets/IGVFDS1724AFUA/) has sequence file(s) [IGVFFI2444NJIP](/sequence-files/IGVFFI2444NJIP/), [IGVFFI4050YOMW](/sequence-files/IGVFFI4050YOMW/), [IGVFFI3375VGEE](/sequence-files/IGVFFI3375VGEE/), [IGVFFI1824RNBS](/sequence-files/IGVFFI1824RNBS/), [IGVFFI1978DGKV](/sequence-files/IGVFFI1978DGKV/), [IGVFFI3221NMVG](/sequence-files/IGVFFI3221NMVG/), [IGVFFI2337HHXE](/sequence-files/IGVFFI2337HHXE/), [IGVFFI4468XYIH](/sequence-files/IGVFFI4468XYIH/), [IGVFFI7236MQBV](/sequence-files/IGVFFI7236MQBV/), [IGVFFI4228LZQG](/sequence-files/IGVFFI4228LZQG/), [IGVFFI4676ZZKO](/sequence-files/IGVFFI4676ZZKO/), [IGVFFI2508CVAU](/sequence-files/IGVFFI2508CVAU/), [IGVFFI2552EWQU](/sequence-files/IGVFFI2552EWQU/), [IGVFFI1357UWRB](/sequence-files/IGVFFI1357UWRB/), [IGVFFI4280RKOM](/sequence-files/IGVFFI4280RKOM/), [IGVFFI3562LFUJ](/sequence-files/IGVFFI3562LFUJ/), [IGVFFI8582LYOD](/sequence-files/IGVFFI8582LYOD/), [IGVFFI1630WZPN](/sequence-files/IGVFFI1630WZPN/), [IGVFFI9872QHGT](/sequence-files/IGVFFI9872QHGT/), [IGVFFI3686AJOK](/sequence-files/IGVFFI3686AJOK/), [IGVFFI2598FZSR](/sequence-files/IGVFFI2598FZSR/), [IGVFFI1007KHIA](/sequence-files/IGVFFI1007KHIA/), [IGVFFI4491KVYP](/sequence-files/IGVFFI4491KVYP/), [IGVFFI6870BLBA](/sequence-files/IGVFFI6870BLBA/), [IGVFFI6352FEST](/sequence-files/IGVFFI6352FEST/), [IGVFFI5218YSSQ](/sequence-files/IGVFFI5218YSSQ/), [IGVFFI7693ODNK](/sequence-files/IGVFFI7693ODNK/), [IGVFFI0849BHOW](/sequence-files/IGVFFI0849BHOW/), [IGVFFI9528LDBC](/sequence-files/IGVFFI9528LDBC/), [IGVFFI2298YXII](/sequence-files/IGVFFI2298YXII/), [IGVFFI9965SKXL](/sequence-files/IGVFFI9965SKXL/), [IGVFFI8723DKVY](/sequence-files/IGVFFI8723DKVY/), [IGVFFI5721NHIP](/sequence-files/IGVFFI5721NHIP/), [IGVFFI7200CQUK](/sequence-files/IGVFFI7200CQUK/), [IGVFFI7133XROH](/sequence-files/IGVFFI7133XROH/), [IGVFFI3045JKYB](/sequence-files/IGVFFI3045JKYB/), [IGVFFI8160SYSC](/sequence-files/IGVFFI8160SYSC/), [IGVFFI0324MEUA](/sequence-files/IGVFFI0324MEUA/), [IGVFFI3142HFGI](/sequence-files/IGVFFI3142HFGI/), [IGVFFI5783KATD](/sequence-files/IGVFFI5783KATD/), [IGVFFI3249ULJY](/sequence-files/IGVFFI3249ULJY/), [IGVFFI7019TDJB](/sequence-files/IGVFFI7019TDJB/), [IGVFFI8101TNOW](/sequence-files/IGVFFI8101TNOW/), [IGVFFI7649FEIT](/sequence-files/IGVFFI7649FEIT/), [IGVFFI8911GKWO](/sequence-files/IGVFFI8911GKWO/), [IGVFFI9957DTEQ](/sequence-files/IGVFFI9957DTEQ/), [IGVFFI0183CMJH](/sequence-files/IGVFFI0183CMJH/), [IGVFFI0708ZDVL](/sequence-files/IGVFFI0708ZDVL/) 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/IGVFDS1724AFUA/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1724AFUA](/auxiliary-sets/IGVFDS1724AFUA/) 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/IGVFDS1724AFUA/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1724AFUA/",
"accession": "IGVFDS1724AFUA",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:45.810308+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": "2023-12-20T23:07:26.789542+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0117NVHQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0117NVHQ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-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_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": "2023-12-13T08:59:10.077106+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": "8c99a469-d50c-428c-bce5-e48843c5d636"
}