{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1769XASS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1769XASS",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-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 [IGVFDS1769XASS](/measurement-sets/IGVFDS1769XASS/) has in progress subobject auxiliary set [IGVFDS2585ICOI](/auxiliary-sets/IGVFDS2585ICOI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1769XASS/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4017CUIN](/in-vitro-systems/IGVFSM4017CUIN/) 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/IGVFSM4017CUIN/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1769XASS](/measurement-sets/IGVFDS1769XASS/) 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/IGVFDS1769XASS/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2585ICOI](/auxiliary-sets/IGVFDS2585ICOI/) has sequence file(s): [IGVFFI0314COCE](/sequence-files/IGVFFI0314COCE/), [IGVFFI3323SYLP](/sequence-files/IGVFFI3323SYLP/), [IGVFFI4861XSVP](/sequence-files/IGVFFI4861XSVP/), [IGVFFI6949EUDY](/sequence-files/IGVFFI6949EUDY/), [IGVFFI3873TNLY](/sequence-files/IGVFFI3873TNLY/), [IGVFFI6004FALS](/sequence-files/IGVFFI6004FALS/), [IGVFFI1740UBUG](/sequence-files/IGVFFI1740UBUG/), [IGVFFI2857NZTI](/sequence-files/IGVFFI2857NZTI/), [IGVFFI6126TQLZ](/sequence-files/IGVFFI6126TQLZ/), [IGVFFI2712KRCM](/sequence-files/IGVFFI2712KRCM/), [IGVFFI8140VKJV](/sequence-files/IGVFFI8140VKJV/), [IGVFFI5311ZOMV](/sequence-files/IGVFFI5311ZOMV/), [IGVFFI5931PPLE](/sequence-files/IGVFFI5931PPLE/), [IGVFFI2518KVBV](/sequence-files/IGVFFI2518KVBV/), [IGVFFI4246EPZW](/sequence-files/IGVFFI4246EPZW/), [IGVFFI9447BCCQ](/sequence-files/IGVFFI9447BCCQ/), [IGVFFI7986YMMD](/sequence-files/IGVFFI7986YMMD/), [IGVFFI6299BGIJ](/sequence-files/IGVFFI6299BGIJ/), [IGVFFI8705TDCF](/sequence-files/IGVFFI8705TDCF/), [IGVFFI3652ZRQC](/sequence-files/IGVFFI3652ZRQC/), [IGVFFI0449QEQC](/sequence-files/IGVFFI0449QEQC/), [IGVFFI5365XJLZ](/sequence-files/IGVFFI5365XJLZ/), [IGVFFI6124INLY](/sequence-files/IGVFFI6124INLY/), [IGVFFI6508ZJZV](/sequence-files/IGVFFI6508ZJZV/), [IGVFFI4627ZLDD](/sequence-files/IGVFFI4627ZLDD/), [IGVFFI7751APGF](/sequence-files/IGVFFI7751APGF/), [IGVFFI8639PCWG](/sequence-files/IGVFFI8639PCWG/), [IGVFFI9959BPYD](/sequence-files/IGVFFI9959BPYD/), [IGVFFI6353YGMX](/sequence-files/IGVFFI6353YGMX/), [IGVFFI5447NVNB](/sequence-files/IGVFFI5447NVNB/), [IGVFFI5138AXYH](/sequence-files/IGVFFI5138AXYH/), [IGVFFI3588NQYI](/sequence-files/IGVFFI3588NQYI/), [IGVFFI6910FIXP](/sequence-files/IGVFFI6910FIXP/), [IGVFFI6928SLKD](/sequence-files/IGVFFI6928SLKD/), [IGVFFI8602GTIC](/sequence-files/IGVFFI8602GTIC/), [IGVFFI1462ZGBE](/sequence-files/IGVFFI1462ZGBE/), [IGVFFI4168VZKE](/sequence-files/IGVFFI4168VZKE/), [IGVFFI4159MCTJ](/sequence-files/IGVFFI4159MCTJ/), [IGVFFI7017SNEL](/sequence-files/IGVFFI7017SNEL/), [IGVFFI9892HLLP](/sequence-files/IGVFFI9892HLLP/), [IGVFFI3452KFFK](/sequence-files/IGVFFI3452KFFK/), [IGVFFI8143HBMT](/sequence-files/IGVFFI8143HBMT/), [IGVFFI4719ZPHD](/sequence-files/IGVFFI4719ZPHD/), [IGVFFI2982ALMP](/sequence-files/IGVFFI2982ALMP/), [IGVFFI5649PBDW](/sequence-files/IGVFFI5649PBDW/), [IGVFFI1964GDMU](/sequence-files/IGVFFI1964GDMU/), [IGVFFI6063DALC](/sequence-files/IGVFFI6063DALC/), [IGVFFI0012ASYH](/sequence-files/IGVFFI0012ASYH/) 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/IGVFDS2585ICOI/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2585ICOI](/auxiliary-sets/IGVFDS2585ICOI/) has sequence file(s) [IGVFFI0314COCE](/sequence-files/IGVFFI0314COCE/), [IGVFFI3323SYLP](/sequence-files/IGVFFI3323SYLP/), [IGVFFI4861XSVP](/sequence-files/IGVFFI4861XSVP/), [IGVFFI6949EUDY](/sequence-files/IGVFFI6949EUDY/), [IGVFFI3873TNLY](/sequence-files/IGVFFI3873TNLY/), [IGVFFI6004FALS](/sequence-files/IGVFFI6004FALS/), [IGVFFI1740UBUG](/sequence-files/IGVFFI1740UBUG/), [IGVFFI2857NZTI](/sequence-files/IGVFFI2857NZTI/), [IGVFFI6126TQLZ](/sequence-files/IGVFFI6126TQLZ/), [IGVFFI2712KRCM](/sequence-files/IGVFFI2712KRCM/), [IGVFFI8140VKJV](/sequence-files/IGVFFI8140VKJV/), [IGVFFI5311ZOMV](/sequence-files/IGVFFI5311ZOMV/), [IGVFFI5931PPLE](/sequence-files/IGVFFI5931PPLE/), [IGVFFI2518KVBV](/sequence-files/IGVFFI2518KVBV/), [IGVFFI4246EPZW](/sequence-files/IGVFFI4246EPZW/), [IGVFFI9447BCCQ](/sequence-files/IGVFFI9447BCCQ/), [IGVFFI7986YMMD](/sequence-files/IGVFFI7986YMMD/), [IGVFFI6299BGIJ](/sequence-files/IGVFFI6299BGIJ/), [IGVFFI8705TDCF](/sequence-files/IGVFFI8705TDCF/), [IGVFFI3652ZRQC](/sequence-files/IGVFFI3652ZRQC/), [IGVFFI0449QEQC](/sequence-files/IGVFFI0449QEQC/), [IGVFFI5365XJLZ](/sequence-files/IGVFFI5365XJLZ/), [IGVFFI6124INLY](/sequence-files/IGVFFI6124INLY/), [IGVFFI6508ZJZV](/sequence-files/IGVFFI6508ZJZV/), [IGVFFI4627ZLDD](/sequence-files/IGVFFI4627ZLDD/), [IGVFFI7751APGF](/sequence-files/IGVFFI7751APGF/), [IGVFFI8639PCWG](/sequence-files/IGVFFI8639PCWG/), [IGVFFI9959BPYD](/sequence-files/IGVFFI9959BPYD/), [IGVFFI6353YGMX](/sequence-files/IGVFFI6353YGMX/), [IGVFFI5447NVNB](/sequence-files/IGVFFI5447NVNB/), [IGVFFI5138AXYH](/sequence-files/IGVFFI5138AXYH/), [IGVFFI3588NQYI](/sequence-files/IGVFFI3588NQYI/), [IGVFFI6910FIXP](/sequence-files/IGVFFI6910FIXP/), [IGVFFI6928SLKD](/sequence-files/IGVFFI6928SLKD/), [IGVFFI8602GTIC](/sequence-files/IGVFFI8602GTIC/), [IGVFFI1462ZGBE](/sequence-files/IGVFFI1462ZGBE/), [IGVFFI4168VZKE](/sequence-files/IGVFFI4168VZKE/), [IGVFFI4159MCTJ](/sequence-files/IGVFFI4159MCTJ/), [IGVFFI7017SNEL](/sequence-files/IGVFFI7017SNEL/), [IGVFFI9892HLLP](/sequence-files/IGVFFI9892HLLP/), [IGVFFI3452KFFK](/sequence-files/IGVFFI3452KFFK/), [IGVFFI8143HBMT](/sequence-files/IGVFFI8143HBMT/), [IGVFFI4719ZPHD](/sequence-files/IGVFFI4719ZPHD/), [IGVFFI2982ALMP](/sequence-files/IGVFFI2982ALMP/), [IGVFFI5649PBDW](/sequence-files/IGVFFI5649PBDW/), [IGVFFI1964GDMU](/sequence-files/IGVFFI1964GDMU/), [IGVFFI6063DALC](/sequence-files/IGVFFI6063DALC/), [IGVFFI0012ASYH](/sequence-files/IGVFFI0012ASYH/) 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/IGVFDS2585ICOI/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2585ICOI](/auxiliary-sets/IGVFDS2585ICOI/) 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/IGVFDS2585ICOI/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2585ICOI/",
"accession": "IGVFDS2585ICOI",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:48:15.493363+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": "2023-12-20T23:08:18.751949+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4017CUIN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4017CUIN",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-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_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 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": "2023-12-13T10:24:49.464491+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": "767ce0ed-5543-428e-bcfd-b7b95b95afa7"
}