{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4758QDZH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4758QDZH",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-BinA_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 [IGVFDS4758QDZH](/measurement-sets/IGVFDS4758QDZH/) has in progress subobject auxiliary set [IGVFDS9285PZZW](/auxiliary-sets/IGVFDS9285PZZW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4758QDZH/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3439ONMT](/in-vitro-systems/IGVFSM3439ONMT/) 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/IGVFSM3439ONMT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4758QDZH](/measurement-sets/IGVFDS4758QDZH/) 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/IGVFDS4758QDZH/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9285PZZW](/auxiliary-sets/IGVFDS9285PZZW/) has sequence file(s) [IGVFFI5348XYNV](/sequence-files/IGVFFI5348XYNV/), [IGVFFI3481XMJW](/sequence-files/IGVFFI3481XMJW/), [IGVFFI4235NPHD](/sequence-files/IGVFFI4235NPHD/), [IGVFFI7705LUWK](/sequence-files/IGVFFI7705LUWK/), [IGVFFI9219QEUS](/sequence-files/IGVFFI9219QEUS/), [IGVFFI8836GRWJ](/sequence-files/IGVFFI8836GRWJ/), [IGVFFI2394HRMV](/sequence-files/IGVFFI2394HRMV/), [IGVFFI5856ILUF](/sequence-files/IGVFFI5856ILUF/), [IGVFFI6699VWFT](/sequence-files/IGVFFI6699VWFT/), [IGVFFI4270AZDB](/sequence-files/IGVFFI4270AZDB/), [IGVFFI6288MIIJ](/sequence-files/IGVFFI6288MIIJ/), [IGVFFI6299MTVY](/sequence-files/IGVFFI6299MTVY/), [IGVFFI1288OQKA](/sequence-files/IGVFFI1288OQKA/), [IGVFFI3477MXHR](/sequence-files/IGVFFI3477MXHR/), [IGVFFI4869HOOI](/sequence-files/IGVFFI4869HOOI/), [IGVFFI2154PRUK](/sequence-files/IGVFFI2154PRUK/), [IGVFFI9076XOXN](/sequence-files/IGVFFI9076XOXN/), [IGVFFI5408HPYW](/sequence-files/IGVFFI5408HPYW/), [IGVFFI0905QVTG](/sequence-files/IGVFFI0905QVTG/), [IGVFFI0654EBOO](/sequence-files/IGVFFI0654EBOO/), [IGVFFI0521GAZK](/sequence-files/IGVFFI0521GAZK/), [IGVFFI0740RQYC](/sequence-files/IGVFFI0740RQYC/), [IGVFFI1210KMIA](/sequence-files/IGVFFI1210KMIA/), [IGVFFI4367PUNP](/sequence-files/IGVFFI4367PUNP/), [IGVFFI7959OGGF](/sequence-files/IGVFFI7959OGGF/), [IGVFFI3223MQXI](/sequence-files/IGVFFI3223MQXI/), [IGVFFI2236EVZE](/sequence-files/IGVFFI2236EVZE/), [IGVFFI3132EMTF](/sequence-files/IGVFFI3132EMTF/), [IGVFFI7872TTIA](/sequence-files/IGVFFI7872TTIA/), [IGVFFI1725YVIS](/sequence-files/IGVFFI1725YVIS/), [IGVFFI1842DABI](/sequence-files/IGVFFI1842DABI/), [IGVFFI3855FHXS](/sequence-files/IGVFFI3855FHXS/), [IGVFFI3342TPRG](/sequence-files/IGVFFI3342TPRG/), [IGVFFI7605DPTL](/sequence-files/IGVFFI7605DPTL/), [IGVFFI4139QHLI](/sequence-files/IGVFFI4139QHLI/), [IGVFFI6079QXYC](/sequence-files/IGVFFI6079QXYC/), [IGVFFI3507ABMI](/sequence-files/IGVFFI3507ABMI/), [IGVFFI3676FHTO](/sequence-files/IGVFFI3676FHTO/), [IGVFFI9591EDPN](/sequence-files/IGVFFI9591EDPN/), [IGVFFI5992WYUF](/sequence-files/IGVFFI5992WYUF/), [IGVFFI0544VRXA](/sequence-files/IGVFFI0544VRXA/), [IGVFFI8251RCJE](/sequence-files/IGVFFI8251RCJE/), [IGVFFI4977AFZI](/sequence-files/IGVFFI4977AFZI/), [IGVFFI2726QDWS](/sequence-files/IGVFFI2726QDWS/), [IGVFFI9546SZHZ](/sequence-files/IGVFFI9546SZHZ/), [IGVFFI0418JNHY](/sequence-files/IGVFFI0418JNHY/), [IGVFFI8012AFLI](/sequence-files/IGVFFI8012AFLI/), [IGVFFI4497LHOW](/sequence-files/IGVFFI4497LHOW/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS9285PZZW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9285PZZW](/auxiliary-sets/IGVFDS9285PZZW/) has sequence file(s): [IGVFFI5348XYNV](/sequence-files/IGVFFI5348XYNV/), [IGVFFI3481XMJW](/sequence-files/IGVFFI3481XMJW/), [IGVFFI4235NPHD](/sequence-files/IGVFFI4235NPHD/), [IGVFFI7705LUWK](/sequence-files/IGVFFI7705LUWK/), [IGVFFI9219QEUS](/sequence-files/IGVFFI9219QEUS/), [IGVFFI8836GRWJ](/sequence-files/IGVFFI8836GRWJ/), [IGVFFI2394HRMV](/sequence-files/IGVFFI2394HRMV/), [IGVFFI5856ILUF](/sequence-files/IGVFFI5856ILUF/), [IGVFFI6699VWFT](/sequence-files/IGVFFI6699VWFT/), [IGVFFI4270AZDB](/sequence-files/IGVFFI4270AZDB/), [IGVFFI6288MIIJ](/sequence-files/IGVFFI6288MIIJ/), [IGVFFI6299MTVY](/sequence-files/IGVFFI6299MTVY/), [IGVFFI1288OQKA](/sequence-files/IGVFFI1288OQKA/), [IGVFFI3477MXHR](/sequence-files/IGVFFI3477MXHR/), [IGVFFI4869HOOI](/sequence-files/IGVFFI4869HOOI/), [IGVFFI2154PRUK](/sequence-files/IGVFFI2154PRUK/), [IGVFFI9076XOXN](/sequence-files/IGVFFI9076XOXN/), [IGVFFI5408HPYW](/sequence-files/IGVFFI5408HPYW/), [IGVFFI0905QVTG](/sequence-files/IGVFFI0905QVTG/), [IGVFFI0654EBOO](/sequence-files/IGVFFI0654EBOO/), [IGVFFI0521GAZK](/sequence-files/IGVFFI0521GAZK/), [IGVFFI0740RQYC](/sequence-files/IGVFFI0740RQYC/), [IGVFFI1210KMIA](/sequence-files/IGVFFI1210KMIA/), [IGVFFI4367PUNP](/sequence-files/IGVFFI4367PUNP/), [IGVFFI7959OGGF](/sequence-files/IGVFFI7959OGGF/), [IGVFFI3223MQXI](/sequence-files/IGVFFI3223MQXI/), [IGVFFI2236EVZE](/sequence-files/IGVFFI2236EVZE/), [IGVFFI3132EMTF](/sequence-files/IGVFFI3132EMTF/), [IGVFFI7872TTIA](/sequence-files/IGVFFI7872TTIA/), [IGVFFI1725YVIS](/sequence-files/IGVFFI1725YVIS/), [IGVFFI1842DABI](/sequence-files/IGVFFI1842DABI/), [IGVFFI3855FHXS](/sequence-files/IGVFFI3855FHXS/), [IGVFFI3342TPRG](/sequence-files/IGVFFI3342TPRG/), [IGVFFI7605DPTL](/sequence-files/IGVFFI7605DPTL/), [IGVFFI4139QHLI](/sequence-files/IGVFFI4139QHLI/), [IGVFFI6079QXYC](/sequence-files/IGVFFI6079QXYC/), [IGVFFI3507ABMI](/sequence-files/IGVFFI3507ABMI/), [IGVFFI3676FHTO](/sequence-files/IGVFFI3676FHTO/), [IGVFFI9591EDPN](/sequence-files/IGVFFI9591EDPN/), [IGVFFI5992WYUF](/sequence-files/IGVFFI5992WYUF/), [IGVFFI0544VRXA](/sequence-files/IGVFFI0544VRXA/), [IGVFFI8251RCJE](/sequence-files/IGVFFI8251RCJE/), [IGVFFI4977AFZI](/sequence-files/IGVFFI4977AFZI/), [IGVFFI2726QDWS](/sequence-files/IGVFFI2726QDWS/), [IGVFFI9546SZHZ](/sequence-files/IGVFFI9546SZHZ/), [IGVFFI0418JNHY](/sequence-files/IGVFFI0418JNHY/), [IGVFFI8012AFLI](/sequence-files/IGVFFI8012AFLI/), [IGVFFI4497LHOW](/sequence-files/IGVFFI4497LHOW/) 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/IGVFDS9285PZZW/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9285PZZW](/auxiliary-sets/IGVFDS9285PZZW/) 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/IGVFDS9285PZZW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9285PZZW/",
"accession": "IGVFDS9285PZZW",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-BinA_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": "2023-12-13T08:48:04.437948+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": "2023-12-20T23:09:07.736419+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3439ONMT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3439ONMT",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-BinA"
],
"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 0-25% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T09:36:28.726568+00:00",
"summary": "prime editing 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": "f03e05ef-1c13-41e4-9227-cee234dac1af"
}