{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5864UGFT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_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 [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) has in progress subobject auxiliary set [IGVFDS8995YDMR](/auxiliary-sets/IGVFDS8995YDMR/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5864UGFT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8995YDMR](/auxiliary-sets/IGVFDS8995YDMR/) has sequence file(s): [IGVFFI4202ZWWK](/sequence-files/IGVFFI4202ZWWK/), [IGVFFI3230WTRR](/sequence-files/IGVFFI3230WTRR/), [IGVFFI7915NGDF](/sequence-files/IGVFFI7915NGDF/), [IGVFFI5738GCOE](/sequence-files/IGVFFI5738GCOE/), [IGVFFI6396HFWS](/sequence-files/IGVFFI6396HFWS/), [IGVFFI6235MNEI](/sequence-files/IGVFFI6235MNEI/), [IGVFFI5305KTDF](/sequence-files/IGVFFI5305KTDF/), [IGVFFI0960MBFN](/sequence-files/IGVFFI0960MBFN/), [IGVFFI5264KOJB](/sequence-files/IGVFFI5264KOJB/), [IGVFFI6767GQPX](/sequence-files/IGVFFI6767GQPX/), [IGVFFI7478BMNB](/sequence-files/IGVFFI7478BMNB/), [IGVFFI8285QUQB](/sequence-files/IGVFFI8285QUQB/), [IGVFFI4285ZZFD](/sequence-files/IGVFFI4285ZZFD/), [IGVFFI9811QIHQ](/sequence-files/IGVFFI9811QIHQ/), [IGVFFI2901MSWB](/sequence-files/IGVFFI2901MSWB/), [IGVFFI2838LQVE](/sequence-files/IGVFFI2838LQVE/) 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/IGVFDS8995YDMR/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) 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/IGVFDS5864UGFT/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) 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/IGVFDS5864UGFT/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8995YDMR](/auxiliary-sets/IGVFDS8995YDMR/) has sequence file(s) [IGVFFI4202ZWWK](/sequence-files/IGVFFI4202ZWWK/), [IGVFFI3230WTRR](/sequence-files/IGVFFI3230WTRR/), [IGVFFI7915NGDF](/sequence-files/IGVFFI7915NGDF/), [IGVFFI5738GCOE](/sequence-files/IGVFFI5738GCOE/), [IGVFFI6396HFWS](/sequence-files/IGVFFI6396HFWS/), [IGVFFI6235MNEI](/sequence-files/IGVFFI6235MNEI/), [IGVFFI5305KTDF](/sequence-files/IGVFFI5305KTDF/), [IGVFFI0960MBFN](/sequence-files/IGVFFI0960MBFN/), [IGVFFI5264KOJB](/sequence-files/IGVFFI5264KOJB/), [IGVFFI6767GQPX](/sequence-files/IGVFFI6767GQPX/), [IGVFFI7478BMNB](/sequence-files/IGVFFI7478BMNB/), [IGVFFI8285QUQB](/sequence-files/IGVFFI8285QUQB/), [IGVFFI4285ZZFD](/sequence-files/IGVFFI4285ZZFD/), [IGVFFI9811QIHQ](/sequence-files/IGVFFI9811QIHQ/), [IGVFFI2901MSWB](/sequence-files/IGVFFI2901MSWB/), [IGVFFI2838LQVE](/sequence-files/IGVFFI2838LQVE/) 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/IGVFDS8995YDMR/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8995YDMR](/auxiliary-sets/IGVFDS8995YDMR/) 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/IGVFDS8995YDMR/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8995YDMR/",
"accession": "IGVFDS8995YDMR",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_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/IGVFDS4745BLLN/",
"accession": "IGVFDS4745BLLN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8290UELV/",
"accession": "IGVFDS8290UELV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS6761PEJX/",
"accession": "IGVFDS6761PEJX",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS6622DPIT/",
"accession": "IGVFDS6622DPIT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS6551IWAB/",
"accession": "IGVFDS6551IWAB",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS5733FUWG/",
"accession": "IGVFDS5733FUWG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS0336ABEV/",
"accession": "IGVFDS0336ABEV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS1783OBDQ/",
"accession": "IGVFDS1783OBDQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS4761MJPK/",
"accession": "IGVFDS4761MJPK",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS6267YRNH/",
"accession": "IGVFDS6267YRNH",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS5699JBLV/",
"accession": "IGVFDS5699JBLV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS3532HUSQ/",
"accession": "IGVFDS3532HUSQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS9665GYVE/",
"accession": "IGVFDS9665GYVE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS0629YEMD/",
"accession": "IGVFDS0629YEMD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS4715UUNW/",
"accession": "IGVFDS4715UUNW",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS1402WRSD/",
"accession": "IGVFDS1402WRSD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS4750CFGI/",
"accession": "IGVFDS4750CFGI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS3537WUVG/",
"accession": "IGVFDS3537WUVG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS9084GQXI/",
"accession": "IGVFDS9084GQXI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS6566NSFE/",
"accession": "IGVFDS6566NSFE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS1674OUCP/",
"accession": "IGVFDS1674OUCP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8517SHZG/",
"accession": "IGVFDS8517SHZG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8736JDCM/",
"accession": "IGVFDS8736JDCM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS2978YQVA/",
"accession": "IGVFDS2978YQVA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS0403DJHI/",
"accession": "IGVFDS0403DJHI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8801DBGC/",
"accession": "IGVFDS8801DBGC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS7403HHLV/",
"accession": "IGVFDS7403HHLV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS3226EEYN/",
"accession": "IGVFDS3226EEYN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8854UNCC/",
"accession": "IGVFDS8854UNCC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS6512WYQI/",
"accession": "IGVFDS6512WYQI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8631OYNB/",
"accession": "IGVFDS8631OYNB",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS9894YFSM/",
"accession": "IGVFDS9894YFSM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinC_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS4761PXVO/",
"accession": "IGVFDS4761PXVO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS1646OXQU/",
"accession": "IGVFDS1646OXQU",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS6147NJBC/",
"accession": "IGVFDS6147NJBC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS7009ITAD/",
"accession": "IGVFDS7009ITAD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS1327XCCU/",
"accession": "IGVFDS1327XCCU",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS0744DITV/",
"accession": "IGVFDS0744DITV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinA_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS8356GTHO/",
"accession": "IGVFDS8356GTHO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinD_AmpliconSequencing"
]
},
{
"@id": "/measurement-sets/IGVFDS7791SSYA/",
"accession": "IGVFDS7791SSYA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinC_AmpliconSequencing"
]
}
],
"creation_timestamp": "2023-11-30T22:49:34.691226+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": "2023-12-20T23:03:34.887828+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7075RRIN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7075RRIN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_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",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T21:30:58.691003+00:00",
"summary": "Variant FlowFISH",
"uuid": "5f789c5b-c158-405c-aa92-fcad5dab2aca"
}