{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9395LATB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9395LATB",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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 [IGVFDS9395LATB](/measurement-sets/IGVFDS9395LATB/) has in progress subobject auxiliary set [IGVFDS4559JCKN](/auxiliary-sets/IGVFDS4559JCKN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9395LATB/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3374KKBT](/in-vitro-systems/IGVFSM3374KKBT/) 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/IGVFSM3374KKBT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4559JCKN](/auxiliary-sets/IGVFDS4559JCKN/) has sequence file(s) [IGVFFI8098CWRA](/sequence-files/IGVFFI8098CWRA/), [IGVFFI0216VAIV](/sequence-files/IGVFFI0216VAIV/), [IGVFFI7166PANR](/sequence-files/IGVFFI7166PANR/), [IGVFFI8231GQFD](/sequence-files/IGVFFI8231GQFD/), [IGVFFI1411YLNG](/sequence-files/IGVFFI1411YLNG/), [IGVFFI4525RJGI](/sequence-files/IGVFFI4525RJGI/), [IGVFFI7160SDGC](/sequence-files/IGVFFI7160SDGC/), [IGVFFI0298OZXA](/sequence-files/IGVFFI0298OZXA/), [IGVFFI4450CBCW](/sequence-files/IGVFFI4450CBCW/), [IGVFFI5407TXSA](/sequence-files/IGVFFI5407TXSA/), [IGVFFI6885QFZI](/sequence-files/IGVFFI6885QFZI/), [IGVFFI5167EBJN](/sequence-files/IGVFFI5167EBJN/), [IGVFFI8071VCVE](/sequence-files/IGVFFI8071VCVE/), [IGVFFI3905HLNM](/sequence-files/IGVFFI3905HLNM/), [IGVFFI0182TEOW](/sequence-files/IGVFFI0182TEOW/), [IGVFFI3966WHXE](/sequence-files/IGVFFI3966WHXE/), [IGVFFI7800TOLG](/sequence-files/IGVFFI7800TOLG/), [IGVFFI3987CPCA](/sequence-files/IGVFFI3987CPCA/), [IGVFFI8836HNSI](/sequence-files/IGVFFI8836HNSI/), [IGVFFI3980YPXC](/sequence-files/IGVFFI3980YPXC/), [IGVFFI0167ZBFE](/sequence-files/IGVFFI0167ZBFE/), [IGVFFI6478TTAZ](/sequence-files/IGVFFI6478TTAZ/), [IGVFFI5016WZNZ](/sequence-files/IGVFFI5016WZNZ/), [IGVFFI9446WBNL](/sequence-files/IGVFFI9446WBNL/), [IGVFFI3595CFEH](/sequence-files/IGVFFI3595CFEH/), [IGVFFI7363TKDP](/sequence-files/IGVFFI7363TKDP/), [IGVFFI8217FYQF](/sequence-files/IGVFFI8217FYQF/), [IGVFFI6243CTZV](/sequence-files/IGVFFI6243CTZV/), [IGVFFI3493PIRA](/sequence-files/IGVFFI3493PIRA/), [IGVFFI4664NHBJ](/sequence-files/IGVFFI4664NHBJ/), [IGVFFI2307YVOG](/sequence-files/IGVFFI2307YVOG/), [IGVFFI7201QPWF](/sequence-files/IGVFFI7201QPWF/), [IGVFFI7271ZKSF](/sequence-files/IGVFFI7271ZKSF/), [IGVFFI2671XRTE](/sequence-files/IGVFFI2671XRTE/), [IGVFFI8843TULP](/sequence-files/IGVFFI8843TULP/), [IGVFFI3648TSTR](/sequence-files/IGVFFI3648TSTR/), [IGVFFI6963PXJG](/sequence-files/IGVFFI6963PXJG/), [IGVFFI8156BYZD](/sequence-files/IGVFFI8156BYZD/), [IGVFFI4376IXAS](/sequence-files/IGVFFI4376IXAS/), [IGVFFI1749YJPM](/sequence-files/IGVFFI1749YJPM/), [IGVFFI9097OZRJ](/sequence-files/IGVFFI9097OZRJ/), [IGVFFI7338IHPP](/sequence-files/IGVFFI7338IHPP/), [IGVFFI2061BASS](/sequence-files/IGVFFI2061BASS/), [IGVFFI3007KARI](/sequence-files/IGVFFI3007KARI/), [IGVFFI6314CLYI](/sequence-files/IGVFFI6314CLYI/), [IGVFFI3723VQEV](/sequence-files/IGVFFI3723VQEV/), [IGVFFI0945QJRS](/sequence-files/IGVFFI0945QJRS/), [IGVFFI9547CDFP](/sequence-files/IGVFFI9547CDFP/) 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/IGVFDS4559JCKN/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4559JCKN](/auxiliary-sets/IGVFDS4559JCKN/) has sequence file(s): [IGVFFI8098CWRA](/sequence-files/IGVFFI8098CWRA/), [IGVFFI0216VAIV](/sequence-files/IGVFFI0216VAIV/), [IGVFFI7166PANR](/sequence-files/IGVFFI7166PANR/), [IGVFFI8231GQFD](/sequence-files/IGVFFI8231GQFD/), [IGVFFI1411YLNG](/sequence-files/IGVFFI1411YLNG/), [IGVFFI4525RJGI](/sequence-files/IGVFFI4525RJGI/), [IGVFFI7160SDGC](/sequence-files/IGVFFI7160SDGC/), [IGVFFI0298OZXA](/sequence-files/IGVFFI0298OZXA/), [IGVFFI4450CBCW](/sequence-files/IGVFFI4450CBCW/), [IGVFFI5407TXSA](/sequence-files/IGVFFI5407TXSA/), [IGVFFI6885QFZI](/sequence-files/IGVFFI6885QFZI/), [IGVFFI5167EBJN](/sequence-files/IGVFFI5167EBJN/), [IGVFFI8071VCVE](/sequence-files/IGVFFI8071VCVE/), [IGVFFI3905HLNM](/sequence-files/IGVFFI3905HLNM/), [IGVFFI0182TEOW](/sequence-files/IGVFFI0182TEOW/), [IGVFFI3966WHXE](/sequence-files/IGVFFI3966WHXE/), [IGVFFI7800TOLG](/sequence-files/IGVFFI7800TOLG/), [IGVFFI3987CPCA](/sequence-files/IGVFFI3987CPCA/), [IGVFFI8836HNSI](/sequence-files/IGVFFI8836HNSI/), [IGVFFI3980YPXC](/sequence-files/IGVFFI3980YPXC/), [IGVFFI0167ZBFE](/sequence-files/IGVFFI0167ZBFE/), [IGVFFI6478TTAZ](/sequence-files/IGVFFI6478TTAZ/), [IGVFFI5016WZNZ](/sequence-files/IGVFFI5016WZNZ/), [IGVFFI9446WBNL](/sequence-files/IGVFFI9446WBNL/), [IGVFFI3595CFEH](/sequence-files/IGVFFI3595CFEH/), [IGVFFI7363TKDP](/sequence-files/IGVFFI7363TKDP/), [IGVFFI8217FYQF](/sequence-files/IGVFFI8217FYQF/), [IGVFFI6243CTZV](/sequence-files/IGVFFI6243CTZV/), [IGVFFI3493PIRA](/sequence-files/IGVFFI3493PIRA/), [IGVFFI4664NHBJ](/sequence-files/IGVFFI4664NHBJ/), [IGVFFI2307YVOG](/sequence-files/IGVFFI2307YVOG/), [IGVFFI7201QPWF](/sequence-files/IGVFFI7201QPWF/), [IGVFFI7271ZKSF](/sequence-files/IGVFFI7271ZKSF/), [IGVFFI2671XRTE](/sequence-files/IGVFFI2671XRTE/), [IGVFFI8843TULP](/sequence-files/IGVFFI8843TULP/), [IGVFFI3648TSTR](/sequence-files/IGVFFI3648TSTR/), [IGVFFI6963PXJG](/sequence-files/IGVFFI6963PXJG/), [IGVFFI8156BYZD](/sequence-files/IGVFFI8156BYZD/), [IGVFFI4376IXAS](/sequence-files/IGVFFI4376IXAS/), [IGVFFI1749YJPM](/sequence-files/IGVFFI1749YJPM/), [IGVFFI9097OZRJ](/sequence-files/IGVFFI9097OZRJ/), [IGVFFI7338IHPP](/sequence-files/IGVFFI7338IHPP/), [IGVFFI2061BASS](/sequence-files/IGVFFI2061BASS/), [IGVFFI3007KARI](/sequence-files/IGVFFI3007KARI/), [IGVFFI6314CLYI](/sequence-files/IGVFFI6314CLYI/), [IGVFFI3723VQEV](/sequence-files/IGVFFI3723VQEV/), [IGVFFI0945QJRS](/sequence-files/IGVFFI0945QJRS/), [IGVFFI9547CDFP](/sequence-files/IGVFFI9547CDFP/) 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/IGVFDS4559JCKN/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9395LATB](/measurement-sets/IGVFDS9395LATB/) 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/IGVFDS9395LATB/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4559JCKN](/auxiliary-sets/IGVFDS4559JCKN/) 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/IGVFDS4559JCKN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4559JCKN/",
"accession": "IGVFDS4559JCKN",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:36.181365+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": "2023-12-20T23:08:01.033636+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3374KKBT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3374KKBT",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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_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 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": "2023-12-13T08:15:33.655746+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": "1c1d604c-d5ef-4890-9ce5-7922a30b02b4"
}