{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1183IGHQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1183IGHQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC_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 [IGVFDS1183IGHQ](/measurement-sets/IGVFDS1183IGHQ/) has in progress subobject auxiliary set [IGVFDS0172IPLG](/auxiliary-sets/IGVFDS0172IPLG/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1183IGHQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3771MMDC](/in-vitro-systems/IGVFSM3771MMDC/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM3771MMDC/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1183IGHQ](/measurement-sets/IGVFDS1183IGHQ/) 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/IGVFDS1183IGHQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0172IPLG](/auxiliary-sets/IGVFDS0172IPLG/) has sequence file(s): [IGVFFI5651JALQ](/sequence-files/IGVFFI5651JALQ/), [IGVFFI3419PXKY](/sequence-files/IGVFFI3419PXKY/), [IGVFFI2657QGHY](/sequence-files/IGVFFI2657QGHY/), [IGVFFI6125FUFL](/sequence-files/IGVFFI6125FUFL/), [IGVFFI2974OLAJ](/sequence-files/IGVFFI2974OLAJ/), [IGVFFI8084FSEC](/sequence-files/IGVFFI8084FSEC/), [IGVFFI7987LULC](/sequence-files/IGVFFI7987LULC/), [IGVFFI2465ILOV](/sequence-files/IGVFFI2465ILOV/), [IGVFFI8137SRKK](/sequence-files/IGVFFI8137SRKK/), [IGVFFI9826RBMH](/sequence-files/IGVFFI9826RBMH/), [IGVFFI7796MJQE](/sequence-files/IGVFFI7796MJQE/), [IGVFFI1518PSCH](/sequence-files/IGVFFI1518PSCH/), [IGVFFI6493GTRD](/sequence-files/IGVFFI6493GTRD/), [IGVFFI5074HBNB](/sequence-files/IGVFFI5074HBNB/), [IGVFFI2468ZLFL](/sequence-files/IGVFFI2468ZLFL/), [IGVFFI8543PVDX](/sequence-files/IGVFFI8543PVDX/), [IGVFFI6152YZDN](/sequence-files/IGVFFI6152YZDN/), [IGVFFI1509CDJI](/sequence-files/IGVFFI1509CDJI/), [IGVFFI9832POMT](/sequence-files/IGVFFI9832POMT/), [IGVFFI4108GXYS](/sequence-files/IGVFFI4108GXYS/), [IGVFFI6462ESFJ](/sequence-files/IGVFFI6462ESFJ/), [IGVFFI9820WVVB](/sequence-files/IGVFFI9820WVVB/), [IGVFFI6676DZDL](/sequence-files/IGVFFI6676DZDL/), [IGVFFI6154QZFM](/sequence-files/IGVFFI6154QZFM/), [IGVFFI2764FWSY](/sequence-files/IGVFFI2764FWSY/), [IGVFFI5847NKOA](/sequence-files/IGVFFI5847NKOA/), [IGVFFI1895LRMV](/sequence-files/IGVFFI1895LRMV/), [IGVFFI0141BQZM](/sequence-files/IGVFFI0141BQZM/), [IGVFFI0149RJDR](/sequence-files/IGVFFI0149RJDR/), [IGVFFI7988IXWV](/sequence-files/IGVFFI7988IXWV/), [IGVFFI3706XGBG](/sequence-files/IGVFFI3706XGBG/), [IGVFFI5006GIAG](/sequence-files/IGVFFI5006GIAG/), [IGVFFI8836ZHYP](/sequence-files/IGVFFI8836ZHYP/), [IGVFFI9153AWHD](/sequence-files/IGVFFI9153AWHD/), [IGVFFI6744TABI](/sequence-files/IGVFFI6744TABI/), [IGVFFI3343MTND](/sequence-files/IGVFFI3343MTND/), [IGVFFI8291ZSJI](/sequence-files/IGVFFI8291ZSJI/), [IGVFFI0762MMIS](/sequence-files/IGVFFI0762MMIS/), [IGVFFI6223MGNU](/sequence-files/IGVFFI6223MGNU/), [IGVFFI3314GITF](/sequence-files/IGVFFI3314GITF/), [IGVFFI5833QCSW](/sequence-files/IGVFFI5833QCSW/), [IGVFFI4504VICY](/sequence-files/IGVFFI4504VICY/), [IGVFFI5654MYJJ](/sequence-files/IGVFFI5654MYJJ/), [IGVFFI1637QHDU](/sequence-files/IGVFFI1637QHDU/), [IGVFFI8025MMQZ](/sequence-files/IGVFFI8025MMQZ/), [IGVFFI9439GRGN](/sequence-files/IGVFFI9439GRGN/), [IGVFFI3728ZQEQ](/sequence-files/IGVFFI3728ZQEQ/), [IGVFFI1698XFQK](/sequence-files/IGVFFI1698XFQK/) 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/IGVFDS0172IPLG/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0172IPLG](/auxiliary-sets/IGVFDS0172IPLG/) has sequence file(s) [IGVFFI5651JALQ](/sequence-files/IGVFFI5651JALQ/), [IGVFFI3419PXKY](/sequence-files/IGVFFI3419PXKY/), [IGVFFI2657QGHY](/sequence-files/IGVFFI2657QGHY/), [IGVFFI6125FUFL](/sequence-files/IGVFFI6125FUFL/), [IGVFFI2974OLAJ](/sequence-files/IGVFFI2974OLAJ/), [IGVFFI8084FSEC](/sequence-files/IGVFFI8084FSEC/), [IGVFFI7987LULC](/sequence-files/IGVFFI7987LULC/), [IGVFFI2465ILOV](/sequence-files/IGVFFI2465ILOV/), [IGVFFI8137SRKK](/sequence-files/IGVFFI8137SRKK/), [IGVFFI9826RBMH](/sequence-files/IGVFFI9826RBMH/), [IGVFFI7796MJQE](/sequence-files/IGVFFI7796MJQE/), [IGVFFI1518PSCH](/sequence-files/IGVFFI1518PSCH/), [IGVFFI6493GTRD](/sequence-files/IGVFFI6493GTRD/), [IGVFFI5074HBNB](/sequence-files/IGVFFI5074HBNB/), [IGVFFI2468ZLFL](/sequence-files/IGVFFI2468ZLFL/), [IGVFFI8543PVDX](/sequence-files/IGVFFI8543PVDX/), [IGVFFI6152YZDN](/sequence-files/IGVFFI6152YZDN/), [IGVFFI1509CDJI](/sequence-files/IGVFFI1509CDJI/), [IGVFFI9832POMT](/sequence-files/IGVFFI9832POMT/), [IGVFFI4108GXYS](/sequence-files/IGVFFI4108GXYS/), [IGVFFI6462ESFJ](/sequence-files/IGVFFI6462ESFJ/), [IGVFFI9820WVVB](/sequence-files/IGVFFI9820WVVB/), [IGVFFI6676DZDL](/sequence-files/IGVFFI6676DZDL/), [IGVFFI6154QZFM](/sequence-files/IGVFFI6154QZFM/), [IGVFFI2764FWSY](/sequence-files/IGVFFI2764FWSY/), [IGVFFI5847NKOA](/sequence-files/IGVFFI5847NKOA/), [IGVFFI1895LRMV](/sequence-files/IGVFFI1895LRMV/), [IGVFFI0141BQZM](/sequence-files/IGVFFI0141BQZM/), [IGVFFI0149RJDR](/sequence-files/IGVFFI0149RJDR/), [IGVFFI7988IXWV](/sequence-files/IGVFFI7988IXWV/), [IGVFFI3706XGBG](/sequence-files/IGVFFI3706XGBG/), [IGVFFI5006GIAG](/sequence-files/IGVFFI5006GIAG/), [IGVFFI8836ZHYP](/sequence-files/IGVFFI8836ZHYP/), [IGVFFI9153AWHD](/sequence-files/IGVFFI9153AWHD/), [IGVFFI6744TABI](/sequence-files/IGVFFI6744TABI/), [IGVFFI3343MTND](/sequence-files/IGVFFI3343MTND/), [IGVFFI8291ZSJI](/sequence-files/IGVFFI8291ZSJI/), [IGVFFI0762MMIS](/sequence-files/IGVFFI0762MMIS/), [IGVFFI6223MGNU](/sequence-files/IGVFFI6223MGNU/), [IGVFFI3314GITF](/sequence-files/IGVFFI3314GITF/), [IGVFFI5833QCSW](/sequence-files/IGVFFI5833QCSW/), [IGVFFI4504VICY](/sequence-files/IGVFFI4504VICY/), [IGVFFI5654MYJJ](/sequence-files/IGVFFI5654MYJJ/), [IGVFFI1637QHDU](/sequence-files/IGVFFI1637QHDU/), [IGVFFI8025MMQZ](/sequence-files/IGVFFI8025MMQZ/), [IGVFFI9439GRGN](/sequence-files/IGVFFI9439GRGN/), [IGVFFI3728ZQEQ](/sequence-files/IGVFFI3728ZQEQ/), [IGVFFI1698XFQK](/sequence-files/IGVFFI1698XFQK/) 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/IGVFDS0172IPLG/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0172IPLG](/auxiliary-sets/IGVFDS0172IPLG/) 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/IGVFDS0172IPLG/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0172IPLG/",
"accession": "IGVFDS0172IPLG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC_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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:48:55.791991+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/IGVFDS5031MNRR/"
],
"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": "2023-12-20T23:05:46.885860+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3771MMDC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3771MMDC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"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 51-75% 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": "2023-12-05T19:59:07.764195+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": "5923baf9-7599-44ef-bf9d-373f1b5c4039"
}