{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4989HPTW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_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 [IGVFDS4989HPTW](/measurement-sets/IGVFDS4989HPTW/) has in progress subobject auxiliary set [IGVFDS1787UFAF](/auxiliary-sets/IGVFDS1787UFAF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4989HPTW/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1787UFAF](/auxiliary-sets/IGVFDS1787UFAF/) has sequence file(s) [IGVFFI5763USVR](/sequence-files/IGVFFI5763USVR/), [IGVFFI0445HZBU](/sequence-files/IGVFFI0445HZBU/), [IGVFFI3409EVBJ](/sequence-files/IGVFFI3409EVBJ/), [IGVFFI8676JDHE](/sequence-files/IGVFFI8676JDHE/), [IGVFFI5926QOUF](/sequence-files/IGVFFI5926QOUF/), [IGVFFI1787VTHF](/sequence-files/IGVFFI1787VTHF/), [IGVFFI7071KMDT](/sequence-files/IGVFFI7071KMDT/), [IGVFFI2581VJGU](/sequence-files/IGVFFI2581VJGU/), [IGVFFI3638DTXQ](/sequence-files/IGVFFI3638DTXQ/), [IGVFFI6121VYZF](/sequence-files/IGVFFI6121VYZF/), [IGVFFI5807UNLW](/sequence-files/IGVFFI5807UNLW/), [IGVFFI4400NUZL](/sequence-files/IGVFFI4400NUZL/), [IGVFFI6091JGXB](/sequence-files/IGVFFI6091JGXB/), [IGVFFI1936ZBLG](/sequence-files/IGVFFI1936ZBLG/), [IGVFFI8924WIBE](/sequence-files/IGVFFI8924WIBE/), [IGVFFI2456ZPNX](/sequence-files/IGVFFI2456ZPNX/) 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/IGVFDS1787UFAF/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1787UFAF](/auxiliary-sets/IGVFDS1787UFAF/) has sequence file(s): [IGVFFI5763USVR](/sequence-files/IGVFFI5763USVR/), [IGVFFI0445HZBU](/sequence-files/IGVFFI0445HZBU/), [IGVFFI3409EVBJ](/sequence-files/IGVFFI3409EVBJ/), [IGVFFI8676JDHE](/sequence-files/IGVFFI8676JDHE/), [IGVFFI5926QOUF](/sequence-files/IGVFFI5926QOUF/), [IGVFFI1787VTHF](/sequence-files/IGVFFI1787VTHF/), [IGVFFI7071KMDT](/sequence-files/IGVFFI7071KMDT/), [IGVFFI2581VJGU](/sequence-files/IGVFFI2581VJGU/), [IGVFFI3638DTXQ](/sequence-files/IGVFFI3638DTXQ/), [IGVFFI6121VYZF](/sequence-files/IGVFFI6121VYZF/), [IGVFFI5807UNLW](/sequence-files/IGVFFI5807UNLW/), [IGVFFI4400NUZL](/sequence-files/IGVFFI4400NUZL/), [IGVFFI6091JGXB](/sequence-files/IGVFFI6091JGXB/), [IGVFFI1936ZBLG](/sequence-files/IGVFFI1936ZBLG/), [IGVFFI8924WIBE](/sequence-files/IGVFFI8924WIBE/), [IGVFFI2456ZPNX](/sequence-files/IGVFFI2456ZPNX/) 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/IGVFDS1787UFAF/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4989HPTW](/measurement-sets/IGVFDS4989HPTW/) 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/IGVFDS4989HPTW/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS4989HPTW](/measurement-sets/IGVFDS4989HPTW/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS4989HPTW/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1787UFAF](/auxiliary-sets/IGVFDS1787UFAF/) 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_for",
"path": "/auxiliary-sets/IGVFDS1787UFAF/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1787UFAF/",
"accession": "IGVFDS1787UFAF",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_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_for": [
{
"@id": "/measurement-sets/IGVFDS8504HJPW/",
"accession": "IGVFDS8504HJPW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS0471SKEE/",
"accession": "IGVFDS0471SKEE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS2059ELNJ/",
"accession": "IGVFDS2059ELNJ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS7083JDYN/",
"accession": "IGVFDS7083JDYN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS6071XLAA/",
"accession": "IGVFDS6071XLAA",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS9915OTKB/",
"accession": "IGVFDS9915OTKB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS6176JWXB/",
"accession": "IGVFDS6176JWXB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS5341DFHM/",
"accession": "IGVFDS5341DFHM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS7933SDSN/",
"accession": "IGVFDS7933SDSN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8050CYYG/",
"accession": "IGVFDS8050CYYG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS2690TJJM/",
"accession": "IGVFDS2690TJJM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS3823MIDB/",
"accession": "IGVFDS3823MIDB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS0621TDYK/",
"accession": "IGVFDS0621TDYK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8825HZQT/",
"accession": "IGVFDS8825HZQT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8518OHPN/",
"accession": "IGVFDS8518OHPN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS9126DKWW/",
"accession": "IGVFDS9126DKWW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS1183IGHQ/",
"accession": "IGVFDS1183IGHQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS5892ADAN/",
"accession": "IGVFDS5892ADAN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS2890JPBI/",
"accession": "IGVFDS2890JPBI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS0816EELG/",
"accession": "IGVFDS0816EELG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS4670KYYZ/",
"accession": "IGVFDS4670KYYZ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8339LZYX/",
"accession": "IGVFDS8339LZYX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS1285SAVV/",
"accession": "IGVFDS1285SAVV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8629CPYB/",
"accession": "IGVFDS8629CPYB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS5601DSMT/",
"accession": "IGVFDS5601DSMT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS6229XAIE/",
"accession": "IGVFDS6229XAIE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS3368XILR/",
"accession": "IGVFDS3368XILR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS5477WNYP/",
"accession": "IGVFDS5477WNYP",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS2074JWFW/",
"accession": "IGVFDS2074JWFW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS9345IHWB/",
"accession": "IGVFDS9345IHWB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS9179GDAL/",
"accession": "IGVFDS9179GDAL",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS2972VXMB/",
"accession": "IGVFDS2972VXMB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS1144XHLC/",
"accession": "IGVFDS1144XHLC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS4386IYQY/",
"accession": "IGVFDS4386IYQY",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS2708HTXW/",
"accession": "IGVFDS2708HTXW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS9571BWRT/",
"accession": "IGVFDS9571BWRT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS4823GFCR/",
"accession": "IGVFDS4823GFCR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS4736IKQS/",
"accession": "IGVFDS4736IKQS",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS7952EIJE/",
"accession": "IGVFDS7952EIJE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS5405RYGU/",
"accession": "IGVFDS5405RYGU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD_AmpliconSequencing"
]
}
],
"creation_timestamp": "2023-11-30T22:48:51.997826+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_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": "2023-12-20T23:03:36.382109+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0894QRYX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0894QRYX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl"
],
"classifications": [
"cell line"
],
"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 modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)",
"taxa": "Homo sapiens"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:40:35.709707+00:00",
"summary": "prime editing Variant FlowFISH",
"uuid": "cb955d48-21de-490a-8627-d9a9ff25daf9"
}