{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7998ZPYH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7998ZPYH",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-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 in vitro system [IGVFSM7747OPJP](/in-vitro-systems/IGVFSM7747OPJP/) 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/IGVFSM7747OPJP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS7998ZPYH](/measurement-sets/IGVFDS7998ZPYH/) has in progress subobject auxiliary set [IGVFDS6568MMJN](/auxiliary-sets/IGVFDS6568MMJN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7998ZPYH/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6568MMJN](/auxiliary-sets/IGVFDS6568MMJN/) has sequence file(s): [IGVFFI1593FMMU](/sequence-files/IGVFFI1593FMMU/), [IGVFFI9448NWMD](/sequence-files/IGVFFI9448NWMD/), [IGVFFI7510QKGR](/sequence-files/IGVFFI7510QKGR/), [IGVFFI3062SVOH](/sequence-files/IGVFFI3062SVOH/), [IGVFFI1086GACK](/sequence-files/IGVFFI1086GACK/), [IGVFFI0809SACR](/sequence-files/IGVFFI0809SACR/), [IGVFFI2867QYPO](/sequence-files/IGVFFI2867QYPO/), [IGVFFI2330IGVA](/sequence-files/IGVFFI2330IGVA/), [IGVFFI2603XKHH](/sequence-files/IGVFFI2603XKHH/), [IGVFFI8636WSSE](/sequence-files/IGVFFI8636WSSE/), [IGVFFI0726LAJS](/sequence-files/IGVFFI0726LAJS/), [IGVFFI2296HYEB](/sequence-files/IGVFFI2296HYEB/), [IGVFFI0421DMUI](/sequence-files/IGVFFI0421DMUI/), [IGVFFI3053DAJE](/sequence-files/IGVFFI3053DAJE/), [IGVFFI3330LGGI](/sequence-files/IGVFFI3330LGGI/), [IGVFFI0606PKDX](/sequence-files/IGVFFI0606PKDX/), [IGVFFI5613OUIK](/sequence-files/IGVFFI5613OUIK/), [IGVFFI1356OUYQ](/sequence-files/IGVFFI1356OUYQ/), [IGVFFI0073HQLF](/sequence-files/IGVFFI0073HQLF/), [IGVFFI7101MFLL](/sequence-files/IGVFFI7101MFLL/), [IGVFFI3027QGFF](/sequence-files/IGVFFI3027QGFF/), [IGVFFI3499IWIJ](/sequence-files/IGVFFI3499IWIJ/), [IGVFFI7974QSSR](/sequence-files/IGVFFI7974QSSR/), [IGVFFI7165VXWQ](/sequence-files/IGVFFI7165VXWQ/), [IGVFFI3023IBUC](/sequence-files/IGVFFI3023IBUC/), [IGVFFI0406HTUZ](/sequence-files/IGVFFI0406HTUZ/), [IGVFFI6078NFZI](/sequence-files/IGVFFI6078NFZI/), [IGVFFI2451VQVH](/sequence-files/IGVFFI2451VQVH/), [IGVFFI6539ZRYD](/sequence-files/IGVFFI6539ZRYD/), [IGVFFI0798MVVE](/sequence-files/IGVFFI0798MVVE/), [IGVFFI0283MNPC](/sequence-files/IGVFFI0283MNPC/), [IGVFFI9531ULYV](/sequence-files/IGVFFI9531ULYV/), [IGVFFI6367PJBT](/sequence-files/IGVFFI6367PJBT/), [IGVFFI8474WSAL](/sequence-files/IGVFFI8474WSAL/), [IGVFFI9073WOEQ](/sequence-files/IGVFFI9073WOEQ/), [IGVFFI9582DGRC](/sequence-files/IGVFFI9582DGRC/), [IGVFFI0015MYIB](/sequence-files/IGVFFI0015MYIB/), [IGVFFI1362ZODM](/sequence-files/IGVFFI1362ZODM/), [IGVFFI4778XPPZ](/sequence-files/IGVFFI4778XPPZ/), [IGVFFI3550YDNB](/sequence-files/IGVFFI3550YDNB/), [IGVFFI4840XGTS](/sequence-files/IGVFFI4840XGTS/), [IGVFFI3388VXUM](/sequence-files/IGVFFI3388VXUM/), [IGVFFI3655UDTY](/sequence-files/IGVFFI3655UDTY/), [IGVFFI0582KZOD](/sequence-files/IGVFFI0582KZOD/), [IGVFFI1734UWFN](/sequence-files/IGVFFI1734UWFN/), [IGVFFI3956YLLC](/sequence-files/IGVFFI3956YLLC/), [IGVFFI5734FTRO](/sequence-files/IGVFFI5734FTRO/), [IGVFFI7712XHLU](/sequence-files/IGVFFI7712XHLU/) 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/IGVFDS6568MMJN/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7998ZPYH](/measurement-sets/IGVFDS7998ZPYH/) 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/IGVFDS7998ZPYH/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6568MMJN](/auxiliary-sets/IGVFDS6568MMJN/) has sequence file(s) [IGVFFI1593FMMU](/sequence-files/IGVFFI1593FMMU/), [IGVFFI9448NWMD](/sequence-files/IGVFFI9448NWMD/), [IGVFFI7510QKGR](/sequence-files/IGVFFI7510QKGR/), [IGVFFI3062SVOH](/sequence-files/IGVFFI3062SVOH/), [IGVFFI1086GACK](/sequence-files/IGVFFI1086GACK/), [IGVFFI0809SACR](/sequence-files/IGVFFI0809SACR/), [IGVFFI2867QYPO](/sequence-files/IGVFFI2867QYPO/), [IGVFFI2330IGVA](/sequence-files/IGVFFI2330IGVA/), [IGVFFI2603XKHH](/sequence-files/IGVFFI2603XKHH/), [IGVFFI8636WSSE](/sequence-files/IGVFFI8636WSSE/), [IGVFFI0726LAJS](/sequence-files/IGVFFI0726LAJS/), [IGVFFI2296HYEB](/sequence-files/IGVFFI2296HYEB/), [IGVFFI0421DMUI](/sequence-files/IGVFFI0421DMUI/), [IGVFFI3053DAJE](/sequence-files/IGVFFI3053DAJE/), [IGVFFI3330LGGI](/sequence-files/IGVFFI3330LGGI/), [IGVFFI0606PKDX](/sequence-files/IGVFFI0606PKDX/), [IGVFFI5613OUIK](/sequence-files/IGVFFI5613OUIK/), [IGVFFI1356OUYQ](/sequence-files/IGVFFI1356OUYQ/), [IGVFFI0073HQLF](/sequence-files/IGVFFI0073HQLF/), [IGVFFI7101MFLL](/sequence-files/IGVFFI7101MFLL/), [IGVFFI3027QGFF](/sequence-files/IGVFFI3027QGFF/), [IGVFFI3499IWIJ](/sequence-files/IGVFFI3499IWIJ/), [IGVFFI7974QSSR](/sequence-files/IGVFFI7974QSSR/), [IGVFFI7165VXWQ](/sequence-files/IGVFFI7165VXWQ/), [IGVFFI3023IBUC](/sequence-files/IGVFFI3023IBUC/), [IGVFFI0406HTUZ](/sequence-files/IGVFFI0406HTUZ/), [IGVFFI6078NFZI](/sequence-files/IGVFFI6078NFZI/), [IGVFFI2451VQVH](/sequence-files/IGVFFI2451VQVH/), [IGVFFI6539ZRYD](/sequence-files/IGVFFI6539ZRYD/), [IGVFFI0798MVVE](/sequence-files/IGVFFI0798MVVE/), [IGVFFI0283MNPC](/sequence-files/IGVFFI0283MNPC/), [IGVFFI9531ULYV](/sequence-files/IGVFFI9531ULYV/), [IGVFFI6367PJBT](/sequence-files/IGVFFI6367PJBT/), [IGVFFI8474WSAL](/sequence-files/IGVFFI8474WSAL/), [IGVFFI9073WOEQ](/sequence-files/IGVFFI9073WOEQ/), [IGVFFI9582DGRC](/sequence-files/IGVFFI9582DGRC/), [IGVFFI0015MYIB](/sequence-files/IGVFFI0015MYIB/), [IGVFFI1362ZODM](/sequence-files/IGVFFI1362ZODM/), [IGVFFI4778XPPZ](/sequence-files/IGVFFI4778XPPZ/), [IGVFFI3550YDNB](/sequence-files/IGVFFI3550YDNB/), [IGVFFI4840XGTS](/sequence-files/IGVFFI4840XGTS/), [IGVFFI3388VXUM](/sequence-files/IGVFFI3388VXUM/), [IGVFFI3655UDTY](/sequence-files/IGVFFI3655UDTY/), [IGVFFI0582KZOD](/sequence-files/IGVFFI0582KZOD/), [IGVFFI1734UWFN](/sequence-files/IGVFFI1734UWFN/), [IGVFFI3956YLLC](/sequence-files/IGVFFI3956YLLC/), [IGVFFI5734FTRO](/sequence-files/IGVFFI5734FTRO/), [IGVFFI7712XHLU](/sequence-files/IGVFFI7712XHLU/) 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/IGVFDS6568MMJN/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6568MMJN](/auxiliary-sets/IGVFDS6568MMJN/) 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/IGVFDS6568MMJN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6568MMJN/",
"accession": "IGVFDS6568MMJN",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-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": "2023-12-13T08:01:41.735510+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": "2023-12-20T23:07:18.312602+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7747OPJP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7747OPJP",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-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": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T08:42:00.226373+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": "0cd6d47f-8fdb-422e-b573-e8c7dc04e995"
}