{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3561FSKT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3561FSKT",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-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 [IGVFDS3561FSKT](/measurement-sets/IGVFDS3561FSKT/) has in progress subobject auxiliary set [IGVFDS2232RVMT](/auxiliary-sets/IGVFDS2232RVMT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3561FSKT/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6493PXNX](/in-vitro-systems/IGVFSM6493PXNX/) 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/IGVFSM6493PXNX/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3561FSKT](/measurement-sets/IGVFDS3561FSKT/) 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/IGVFDS3561FSKT/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2232RVMT](/auxiliary-sets/IGVFDS2232RVMT/) has sequence file(s): [IGVFFI2234KVEY](/sequence-files/IGVFFI2234KVEY/), [IGVFFI5775YFXO](/sequence-files/IGVFFI5775YFXO/), [IGVFFI1192CZMA](/sequence-files/IGVFFI1192CZMA/), [IGVFFI1448KYTZ](/sequence-files/IGVFFI1448KYTZ/), [IGVFFI9065PZZH](/sequence-files/IGVFFI9065PZZH/), [IGVFFI4462SQYP](/sequence-files/IGVFFI4462SQYP/), [IGVFFI3052URKY](/sequence-files/IGVFFI3052URKY/), [IGVFFI4017BJXN](/sequence-files/IGVFFI4017BJXN/), [IGVFFI7566GBAL](/sequence-files/IGVFFI7566GBAL/), [IGVFFI9646SAZO](/sequence-files/IGVFFI9646SAZO/), [IGVFFI3790IBMZ](/sequence-files/IGVFFI3790IBMZ/), [IGVFFI0423OGGT](/sequence-files/IGVFFI0423OGGT/), [IGVFFI0889MEKX](/sequence-files/IGVFFI0889MEKX/), [IGVFFI8689QHOK](/sequence-files/IGVFFI8689QHOK/), [IGVFFI5768OQOS](/sequence-files/IGVFFI5768OQOS/), [IGVFFI0760BYPV](/sequence-files/IGVFFI0760BYPV/), [IGVFFI5971ZSND](/sequence-files/IGVFFI5971ZSND/), [IGVFFI2116SCVI](/sequence-files/IGVFFI2116SCVI/), [IGVFFI8287PFCZ](/sequence-files/IGVFFI8287PFCZ/), [IGVFFI1734CSWX](/sequence-files/IGVFFI1734CSWX/), [IGVFFI6051EHGV](/sequence-files/IGVFFI6051EHGV/), [IGVFFI3851TWWR](/sequence-files/IGVFFI3851TWWR/), [IGVFFI8051AMOU](/sequence-files/IGVFFI8051AMOU/), [IGVFFI5902HDIW](/sequence-files/IGVFFI5902HDIW/), [IGVFFI2830OUDU](/sequence-files/IGVFFI2830OUDU/), [IGVFFI2801ZLNU](/sequence-files/IGVFFI2801ZLNU/), [IGVFFI3658NCGQ](/sequence-files/IGVFFI3658NCGQ/), [IGVFFI3530LFPI](/sequence-files/IGVFFI3530LFPI/), [IGVFFI1166BZPS](/sequence-files/IGVFFI1166BZPS/), [IGVFFI2863GSZO](/sequence-files/IGVFFI2863GSZO/), [IGVFFI2613DASS](/sequence-files/IGVFFI2613DASS/), [IGVFFI0727ZNCW](/sequence-files/IGVFFI0727ZNCW/), [IGVFFI4136FEKU](/sequence-files/IGVFFI4136FEKU/), [IGVFFI4068RZWC](/sequence-files/IGVFFI4068RZWC/), [IGVFFI5875UYYV](/sequence-files/IGVFFI5875UYYV/), [IGVFFI0022VIOD](/sequence-files/IGVFFI0022VIOD/), [IGVFFI0588KREN](/sequence-files/IGVFFI0588KREN/), [IGVFFI7638OJAS](/sequence-files/IGVFFI7638OJAS/), [IGVFFI2552QGVT](/sequence-files/IGVFFI2552QGVT/), [IGVFFI6527UGIB](/sequence-files/IGVFFI6527UGIB/), [IGVFFI6396IJQM](/sequence-files/IGVFFI6396IJQM/), [IGVFFI3825QDEV](/sequence-files/IGVFFI3825QDEV/), [IGVFFI0622ZAUE](/sequence-files/IGVFFI0622ZAUE/), [IGVFFI7273QMDX](/sequence-files/IGVFFI7273QMDX/), [IGVFFI4028RQVM](/sequence-files/IGVFFI4028RQVM/), [IGVFFI3399IAHG](/sequence-files/IGVFFI3399IAHG/), [IGVFFI8986LQYS](/sequence-files/IGVFFI8986LQYS/), [IGVFFI2983HFEB](/sequence-files/IGVFFI2983HFEB/) 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/IGVFDS2232RVMT/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2232RVMT](/auxiliary-sets/IGVFDS2232RVMT/) has sequence file(s) [IGVFFI2234KVEY](/sequence-files/IGVFFI2234KVEY/), [IGVFFI5775YFXO](/sequence-files/IGVFFI5775YFXO/), [IGVFFI1192CZMA](/sequence-files/IGVFFI1192CZMA/), [IGVFFI1448KYTZ](/sequence-files/IGVFFI1448KYTZ/), [IGVFFI9065PZZH](/sequence-files/IGVFFI9065PZZH/), [IGVFFI4462SQYP](/sequence-files/IGVFFI4462SQYP/), [IGVFFI3052URKY](/sequence-files/IGVFFI3052URKY/), [IGVFFI4017BJXN](/sequence-files/IGVFFI4017BJXN/), [IGVFFI7566GBAL](/sequence-files/IGVFFI7566GBAL/), [IGVFFI9646SAZO](/sequence-files/IGVFFI9646SAZO/), [IGVFFI3790IBMZ](/sequence-files/IGVFFI3790IBMZ/), [IGVFFI0423OGGT](/sequence-files/IGVFFI0423OGGT/), [IGVFFI0889MEKX](/sequence-files/IGVFFI0889MEKX/), [IGVFFI8689QHOK](/sequence-files/IGVFFI8689QHOK/), [IGVFFI5768OQOS](/sequence-files/IGVFFI5768OQOS/), [IGVFFI0760BYPV](/sequence-files/IGVFFI0760BYPV/), [IGVFFI5971ZSND](/sequence-files/IGVFFI5971ZSND/), [IGVFFI2116SCVI](/sequence-files/IGVFFI2116SCVI/), [IGVFFI8287PFCZ](/sequence-files/IGVFFI8287PFCZ/), [IGVFFI1734CSWX](/sequence-files/IGVFFI1734CSWX/), [IGVFFI6051EHGV](/sequence-files/IGVFFI6051EHGV/), [IGVFFI3851TWWR](/sequence-files/IGVFFI3851TWWR/), [IGVFFI8051AMOU](/sequence-files/IGVFFI8051AMOU/), [IGVFFI5902HDIW](/sequence-files/IGVFFI5902HDIW/), [IGVFFI2830OUDU](/sequence-files/IGVFFI2830OUDU/), [IGVFFI2801ZLNU](/sequence-files/IGVFFI2801ZLNU/), [IGVFFI3658NCGQ](/sequence-files/IGVFFI3658NCGQ/), [IGVFFI3530LFPI](/sequence-files/IGVFFI3530LFPI/), [IGVFFI1166BZPS](/sequence-files/IGVFFI1166BZPS/), [IGVFFI2863GSZO](/sequence-files/IGVFFI2863GSZO/), [IGVFFI2613DASS](/sequence-files/IGVFFI2613DASS/), [IGVFFI0727ZNCW](/sequence-files/IGVFFI0727ZNCW/), [IGVFFI4136FEKU](/sequence-files/IGVFFI4136FEKU/), [IGVFFI4068RZWC](/sequence-files/IGVFFI4068RZWC/), [IGVFFI5875UYYV](/sequence-files/IGVFFI5875UYYV/), [IGVFFI0022VIOD](/sequence-files/IGVFFI0022VIOD/), [IGVFFI0588KREN](/sequence-files/IGVFFI0588KREN/), [IGVFFI7638OJAS](/sequence-files/IGVFFI7638OJAS/), [IGVFFI2552QGVT](/sequence-files/IGVFFI2552QGVT/), [IGVFFI6527UGIB](/sequence-files/IGVFFI6527UGIB/), [IGVFFI6396IJQM](/sequence-files/IGVFFI6396IJQM/), [IGVFFI3825QDEV](/sequence-files/IGVFFI3825QDEV/), [IGVFFI0622ZAUE](/sequence-files/IGVFFI0622ZAUE/), [IGVFFI7273QMDX](/sequence-files/IGVFFI7273QMDX/), [IGVFFI4028RQVM](/sequence-files/IGVFFI4028RQVM/), [IGVFFI3399IAHG](/sequence-files/IGVFFI3399IAHG/), [IGVFFI8986LQYS](/sequence-files/IGVFFI8986LQYS/), [IGVFFI2983HFEB](/sequence-files/IGVFFI2983HFEB/) 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/IGVFDS2232RVMT/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2232RVMT](/auxiliary-sets/IGVFDS2232RVMT/) 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/IGVFDS2232RVMT/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2232RVMT/",
"accession": "IGVFDS2232RVMT",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:48:02.639900+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": "2023-12-20T23:08:14.263327+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6493PXNX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6493PXNX",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-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_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": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T09:18:55.115702+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": "4ccd7492-29b5-4475-8921-861efcf80a2d"
}