{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6384OLQB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6384OLQB",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-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 in vitro system [IGVFSM7963WTMN](/in-vitro-systems/IGVFSM7963WTMN/) 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/IGVFSM7963WTMN/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6384OLQB](/measurement-sets/IGVFDS6384OLQB/) has in progress subobject auxiliary set [IGVFDS8092GWMN](/auxiliary-sets/IGVFDS8092GWMN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6384OLQB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6384OLQB](/measurement-sets/IGVFDS6384OLQB/) 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/IGVFDS6384OLQB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8092GWMN](/auxiliary-sets/IGVFDS8092GWMN/) has sequence file(s): [IGVFFI2661NEMR](/sequence-files/IGVFFI2661NEMR/), [IGVFFI2320TDED](/sequence-files/IGVFFI2320TDED/), [IGVFFI3505NULA](/sequence-files/IGVFFI3505NULA/), [IGVFFI8865BGDP](/sequence-files/IGVFFI8865BGDP/), [IGVFFI9144TFFY](/sequence-files/IGVFFI9144TFFY/), [IGVFFI1093ZXXW](/sequence-files/IGVFFI1093ZXXW/), [IGVFFI7945EHVE](/sequence-files/IGVFFI7945EHVE/), [IGVFFI0075NRDV](/sequence-files/IGVFFI0075NRDV/), [IGVFFI3130ANMH](/sequence-files/IGVFFI3130ANMH/), [IGVFFI4914VBPX](/sequence-files/IGVFFI4914VBPX/), [IGVFFI1320HCEW](/sequence-files/IGVFFI1320HCEW/), [IGVFFI3654WJLA](/sequence-files/IGVFFI3654WJLA/), [IGVFFI8514FZSX](/sequence-files/IGVFFI8514FZSX/), [IGVFFI2654GZWO](/sequence-files/IGVFFI2654GZWO/), [IGVFFI6091ZCGZ](/sequence-files/IGVFFI6091ZCGZ/), [IGVFFI6527TIMK](/sequence-files/IGVFFI6527TIMK/), [IGVFFI1313ZANK](/sequence-files/IGVFFI1313ZANK/), [IGVFFI1442ZZUG](/sequence-files/IGVFFI1442ZZUG/), [IGVFFI0640JQJC](/sequence-files/IGVFFI0640JQJC/), [IGVFFI7588HJWX](/sequence-files/IGVFFI7588HJWX/), [IGVFFI5943CFOT](/sequence-files/IGVFFI5943CFOT/), [IGVFFI5885OHLF](/sequence-files/IGVFFI5885OHLF/), [IGVFFI2215WSNR](/sequence-files/IGVFFI2215WSNR/), [IGVFFI2661BIIB](/sequence-files/IGVFFI2661BIIB/), [IGVFFI1526LMUD](/sequence-files/IGVFFI1526LMUD/), [IGVFFI4175NGXC](/sequence-files/IGVFFI4175NGXC/), [IGVFFI9685WFZP](/sequence-files/IGVFFI9685WFZP/), [IGVFFI8535SIFG](/sequence-files/IGVFFI8535SIFG/), [IGVFFI0704EXUX](/sequence-files/IGVFFI0704EXUX/), [IGVFFI0775QLSE](/sequence-files/IGVFFI0775QLSE/), [IGVFFI8119VIHT](/sequence-files/IGVFFI8119VIHT/), [IGVFFI4048ISZR](/sequence-files/IGVFFI4048ISZR/), [IGVFFI3190WRDA](/sequence-files/IGVFFI3190WRDA/), [IGVFFI3846NYDO](/sequence-files/IGVFFI3846NYDO/), [IGVFFI6406SKBK](/sequence-files/IGVFFI6406SKBK/), [IGVFFI5474KBUG](/sequence-files/IGVFFI5474KBUG/), [IGVFFI0675BFFI](/sequence-files/IGVFFI0675BFFI/), [IGVFFI5553GWNR](/sequence-files/IGVFFI5553GWNR/), [IGVFFI0477NWCQ](/sequence-files/IGVFFI0477NWCQ/), [IGVFFI3480EYXY](/sequence-files/IGVFFI3480EYXY/), [IGVFFI7588IUSC](/sequence-files/IGVFFI7588IUSC/), [IGVFFI2148IVJH](/sequence-files/IGVFFI2148IVJH/), [IGVFFI0285QVEW](/sequence-files/IGVFFI0285QVEW/), [IGVFFI7779NNCB](/sequence-files/IGVFFI7779NNCB/), [IGVFFI7457BTGG](/sequence-files/IGVFFI7457BTGG/), [IGVFFI5214BCWE](/sequence-files/IGVFFI5214BCWE/), [IGVFFI4623DAEQ](/sequence-files/IGVFFI4623DAEQ/), [IGVFFI1021OHWZ](/sequence-files/IGVFFI1021OHWZ/) 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/IGVFDS8092GWMN/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8092GWMN](/auxiliary-sets/IGVFDS8092GWMN/) has sequence file(s) [IGVFFI2661NEMR](/sequence-files/IGVFFI2661NEMR/), [IGVFFI2320TDED](/sequence-files/IGVFFI2320TDED/), [IGVFFI3505NULA](/sequence-files/IGVFFI3505NULA/), [IGVFFI8865BGDP](/sequence-files/IGVFFI8865BGDP/), [IGVFFI9144TFFY](/sequence-files/IGVFFI9144TFFY/), [IGVFFI1093ZXXW](/sequence-files/IGVFFI1093ZXXW/), [IGVFFI7945EHVE](/sequence-files/IGVFFI7945EHVE/), [IGVFFI0075NRDV](/sequence-files/IGVFFI0075NRDV/), [IGVFFI3130ANMH](/sequence-files/IGVFFI3130ANMH/), [IGVFFI4914VBPX](/sequence-files/IGVFFI4914VBPX/), [IGVFFI1320HCEW](/sequence-files/IGVFFI1320HCEW/), [IGVFFI3654WJLA](/sequence-files/IGVFFI3654WJLA/), [IGVFFI8514FZSX](/sequence-files/IGVFFI8514FZSX/), [IGVFFI2654GZWO](/sequence-files/IGVFFI2654GZWO/), [IGVFFI6091ZCGZ](/sequence-files/IGVFFI6091ZCGZ/), [IGVFFI6527TIMK](/sequence-files/IGVFFI6527TIMK/), [IGVFFI1313ZANK](/sequence-files/IGVFFI1313ZANK/), [IGVFFI1442ZZUG](/sequence-files/IGVFFI1442ZZUG/), [IGVFFI0640JQJC](/sequence-files/IGVFFI0640JQJC/), [IGVFFI7588HJWX](/sequence-files/IGVFFI7588HJWX/), [IGVFFI5943CFOT](/sequence-files/IGVFFI5943CFOT/), [IGVFFI5885OHLF](/sequence-files/IGVFFI5885OHLF/), [IGVFFI2215WSNR](/sequence-files/IGVFFI2215WSNR/), [IGVFFI2661BIIB](/sequence-files/IGVFFI2661BIIB/), [IGVFFI1526LMUD](/sequence-files/IGVFFI1526LMUD/), [IGVFFI4175NGXC](/sequence-files/IGVFFI4175NGXC/), [IGVFFI9685WFZP](/sequence-files/IGVFFI9685WFZP/), [IGVFFI8535SIFG](/sequence-files/IGVFFI8535SIFG/), [IGVFFI0704EXUX](/sequence-files/IGVFFI0704EXUX/), [IGVFFI0775QLSE](/sequence-files/IGVFFI0775QLSE/), [IGVFFI8119VIHT](/sequence-files/IGVFFI8119VIHT/), [IGVFFI4048ISZR](/sequence-files/IGVFFI4048ISZR/), [IGVFFI3190WRDA](/sequence-files/IGVFFI3190WRDA/), [IGVFFI3846NYDO](/sequence-files/IGVFFI3846NYDO/), [IGVFFI6406SKBK](/sequence-files/IGVFFI6406SKBK/), [IGVFFI5474KBUG](/sequence-files/IGVFFI5474KBUG/), [IGVFFI0675BFFI](/sequence-files/IGVFFI0675BFFI/), [IGVFFI5553GWNR](/sequence-files/IGVFFI5553GWNR/), [IGVFFI0477NWCQ](/sequence-files/IGVFFI0477NWCQ/), [IGVFFI3480EYXY](/sequence-files/IGVFFI3480EYXY/), [IGVFFI7588IUSC](/sequence-files/IGVFFI7588IUSC/), [IGVFFI2148IVJH](/sequence-files/IGVFFI2148IVJH/), [IGVFFI0285QVEW](/sequence-files/IGVFFI0285QVEW/), [IGVFFI7779NNCB](/sequence-files/IGVFFI7779NNCB/), [IGVFFI7457BTGG](/sequence-files/IGVFFI7457BTGG/), [IGVFFI5214BCWE](/sequence-files/IGVFFI5214BCWE/), [IGVFFI4623DAEQ](/sequence-files/IGVFFI4623DAEQ/), [IGVFFI1021OHWZ](/sequence-files/IGVFFI1021OHWZ/) 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/IGVFDS8092GWMN/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8092GWMN](/auxiliary-sets/IGVFDS8092GWMN/) 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/IGVFDS8092GWMN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8092GWMN/",
"accession": "IGVFDS8092GWMN",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-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": "2023-12-13T08:01:47.231161+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": "2023-12-20T23:07:53.754657+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7963WTMN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7963WTMN",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-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": "2023-12-13T09:07:34.643349+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": "8b72cac0-220b-4b8f-9f1f-09aa210620ff"
}