{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6761PEJX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6761PEJX",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinB_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 [IGVFDS6761PEJX](/measurement-sets/IGVFDS6761PEJX/) has in progress subobject auxiliary set [IGVFDS8755CPJA](/auxiliary-sets/IGVFDS8755CPJA/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6761PEJX/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8901HJRO](/in-vitro-systems/IGVFSM8901HJRO/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8901HJRO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8755CPJA](/auxiliary-sets/IGVFDS8755CPJA/) has sequence file(s): [IGVFFI1448XSES](/sequence-files/IGVFFI1448XSES/), [IGVFFI7655UVBA](/sequence-files/IGVFFI7655UVBA/), [IGVFFI4410VWGU](/sequence-files/IGVFFI4410VWGU/), [IGVFFI7872VAHJ](/sequence-files/IGVFFI7872VAHJ/), [IGVFFI3748PUHZ](/sequence-files/IGVFFI3748PUHZ/), [IGVFFI7626HTCH](/sequence-files/IGVFFI7626HTCH/), [IGVFFI3919RUKZ](/sequence-files/IGVFFI3919RUKZ/), [IGVFFI5301MCKD](/sequence-files/IGVFFI5301MCKD/), [IGVFFI2139CBKN](/sequence-files/IGVFFI2139CBKN/), [IGVFFI4405EQEJ](/sequence-files/IGVFFI4405EQEJ/), [IGVFFI9737LYQI](/sequence-files/IGVFFI9737LYQI/), [IGVFFI6148FVCP](/sequence-files/IGVFFI6148FVCP/), [IGVFFI0611WYEU](/sequence-files/IGVFFI0611WYEU/), [IGVFFI4035VZLU](/sequence-files/IGVFFI4035VZLU/), [IGVFFI6029DDWZ](/sequence-files/IGVFFI6029DDWZ/), [IGVFFI7158DPXM](/sequence-files/IGVFFI7158DPXM/), [IGVFFI7621LVTV](/sequence-files/IGVFFI7621LVTV/), [IGVFFI5518ROJI](/sequence-files/IGVFFI5518ROJI/), [IGVFFI7150FMCK](/sequence-files/IGVFFI7150FMCK/), [IGVFFI8979DCDR](/sequence-files/IGVFFI8979DCDR/), [IGVFFI0167DNDM](/sequence-files/IGVFFI0167DNDM/), [IGVFFI5647THQB](/sequence-files/IGVFFI5647THQB/), [IGVFFI9845UTCQ](/sequence-files/IGVFFI9845UTCQ/), [IGVFFI2213DFCW](/sequence-files/IGVFFI2213DFCW/), [IGVFFI1479BCAI](/sequence-files/IGVFFI1479BCAI/), [IGVFFI6382TDKO](/sequence-files/IGVFFI6382TDKO/), [IGVFFI2939DOZQ](/sequence-files/IGVFFI2939DOZQ/), [IGVFFI8367LJPF](/sequence-files/IGVFFI8367LJPF/), [IGVFFI9035FHIA](/sequence-files/IGVFFI9035FHIA/), [IGVFFI3117SQOM](/sequence-files/IGVFFI3117SQOM/), [IGVFFI1177WAGF](/sequence-files/IGVFFI1177WAGF/), [IGVFFI8597TFDI](/sequence-files/IGVFFI8597TFDI/), [IGVFFI7939DHUP](/sequence-files/IGVFFI7939DHUP/), [IGVFFI6205NMRV](/sequence-files/IGVFFI6205NMRV/), [IGVFFI0535KATF](/sequence-files/IGVFFI0535KATF/), [IGVFFI1618PTZA](/sequence-files/IGVFFI1618PTZA/), [IGVFFI0693ACZE](/sequence-files/IGVFFI0693ACZE/), [IGVFFI6601JEKP](/sequence-files/IGVFFI6601JEKP/), [IGVFFI6499XVYU](/sequence-files/IGVFFI6499XVYU/), [IGVFFI0299BKSG](/sequence-files/IGVFFI0299BKSG/), [IGVFFI2512OOCN](/sequence-files/IGVFFI2512OOCN/), [IGVFFI9941OBET](/sequence-files/IGVFFI9941OBET/), [IGVFFI5606PIHM](/sequence-files/IGVFFI5606PIHM/), [IGVFFI2778UYBW](/sequence-files/IGVFFI2778UYBW/), [IGVFFI9309XYJY](/sequence-files/IGVFFI9309XYJY/), [IGVFFI1457MHPI](/sequence-files/IGVFFI1457MHPI/), [IGVFFI4806HPCX](/sequence-files/IGVFFI4806HPCX/), [IGVFFI1743DYUF](/sequence-files/IGVFFI1743DYUF/) 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/IGVFDS8755CPJA/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6761PEJX](/measurement-sets/IGVFDS6761PEJX/) 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/IGVFDS6761PEJX/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8755CPJA](/auxiliary-sets/IGVFDS8755CPJA/) has sequence file(s) [IGVFFI1448XSES](/sequence-files/IGVFFI1448XSES/), [IGVFFI7655UVBA](/sequence-files/IGVFFI7655UVBA/), [IGVFFI4410VWGU](/sequence-files/IGVFFI4410VWGU/), [IGVFFI7872VAHJ](/sequence-files/IGVFFI7872VAHJ/), [IGVFFI3748PUHZ](/sequence-files/IGVFFI3748PUHZ/), [IGVFFI7626HTCH](/sequence-files/IGVFFI7626HTCH/), [IGVFFI3919RUKZ](/sequence-files/IGVFFI3919RUKZ/), [IGVFFI5301MCKD](/sequence-files/IGVFFI5301MCKD/), [IGVFFI2139CBKN](/sequence-files/IGVFFI2139CBKN/), [IGVFFI4405EQEJ](/sequence-files/IGVFFI4405EQEJ/), [IGVFFI9737LYQI](/sequence-files/IGVFFI9737LYQI/), [IGVFFI6148FVCP](/sequence-files/IGVFFI6148FVCP/), [IGVFFI0611WYEU](/sequence-files/IGVFFI0611WYEU/), [IGVFFI4035VZLU](/sequence-files/IGVFFI4035VZLU/), [IGVFFI6029DDWZ](/sequence-files/IGVFFI6029DDWZ/), [IGVFFI7158DPXM](/sequence-files/IGVFFI7158DPXM/), [IGVFFI7621LVTV](/sequence-files/IGVFFI7621LVTV/), [IGVFFI5518ROJI](/sequence-files/IGVFFI5518ROJI/), [IGVFFI7150FMCK](/sequence-files/IGVFFI7150FMCK/), [IGVFFI8979DCDR](/sequence-files/IGVFFI8979DCDR/), [IGVFFI0167DNDM](/sequence-files/IGVFFI0167DNDM/), [IGVFFI5647THQB](/sequence-files/IGVFFI5647THQB/), [IGVFFI9845UTCQ](/sequence-files/IGVFFI9845UTCQ/), [IGVFFI2213DFCW](/sequence-files/IGVFFI2213DFCW/), [IGVFFI1479BCAI](/sequence-files/IGVFFI1479BCAI/), [IGVFFI6382TDKO](/sequence-files/IGVFFI6382TDKO/), [IGVFFI2939DOZQ](/sequence-files/IGVFFI2939DOZQ/), [IGVFFI8367LJPF](/sequence-files/IGVFFI8367LJPF/), [IGVFFI9035FHIA](/sequence-files/IGVFFI9035FHIA/), [IGVFFI3117SQOM](/sequence-files/IGVFFI3117SQOM/), [IGVFFI1177WAGF](/sequence-files/IGVFFI1177WAGF/), [IGVFFI8597TFDI](/sequence-files/IGVFFI8597TFDI/), [IGVFFI7939DHUP](/sequence-files/IGVFFI7939DHUP/), [IGVFFI6205NMRV](/sequence-files/IGVFFI6205NMRV/), [IGVFFI0535KATF](/sequence-files/IGVFFI0535KATF/), [IGVFFI1618PTZA](/sequence-files/IGVFFI1618PTZA/), [IGVFFI0693ACZE](/sequence-files/IGVFFI0693ACZE/), [IGVFFI6601JEKP](/sequence-files/IGVFFI6601JEKP/), [IGVFFI6499XVYU](/sequence-files/IGVFFI6499XVYU/), [IGVFFI0299BKSG](/sequence-files/IGVFFI0299BKSG/), [IGVFFI2512OOCN](/sequence-files/IGVFFI2512OOCN/), [IGVFFI9941OBET](/sequence-files/IGVFFI9941OBET/), [IGVFFI5606PIHM](/sequence-files/IGVFFI5606PIHM/), [IGVFFI2778UYBW](/sequence-files/IGVFFI2778UYBW/), [IGVFFI9309XYJY](/sequence-files/IGVFFI9309XYJY/), [IGVFFI1457MHPI](/sequence-files/IGVFFI1457MHPI/), [IGVFFI4806HPCX](/sequence-files/IGVFFI4806HPCX/), [IGVFFI1743DYUF](/sequence-files/IGVFFI1743DYUF/) 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/IGVFDS8755CPJA/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8755CPJA](/auxiliary-sets/IGVFDS8755CPJA/) 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/IGVFDS8755CPJA/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8755CPJA/",
"accession": "IGVFDS8755CPJA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinB_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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:43.735812+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/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:16.314428+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8901HJRO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8901HJRO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinB"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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 26-50% 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": "2023-12-05T20:39:03.322182+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": "175fce4c-b6d0-4045-9933-85ec86858835"
}