{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0403DJHI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0403DJHI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-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 [IGVFDS0403DJHI](/measurement-sets/IGVFDS0403DJHI/) has in progress subobject auxiliary set [IGVFDS0791ADVW](/auxiliary-sets/IGVFDS0791ADVW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0403DJHI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7954ICIY](/in-vitro-systems/IGVFSM7954ICIY/) 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/IGVFSM7954ICIY/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0403DJHI](/measurement-sets/IGVFDS0403DJHI/) 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/IGVFDS0403DJHI/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0791ADVW](/auxiliary-sets/IGVFDS0791ADVW/) has sequence file(s): [IGVFFI8269CZGN](/sequence-files/IGVFFI8269CZGN/), [IGVFFI5970VSBC](/sequence-files/IGVFFI5970VSBC/), [IGVFFI5277SPHD](/sequence-files/IGVFFI5277SPHD/), [IGVFFI7239KLVT](/sequence-files/IGVFFI7239KLVT/), [IGVFFI4629NALN](/sequence-files/IGVFFI4629NALN/), [IGVFFI5202JJWF](/sequence-files/IGVFFI5202JJWF/), [IGVFFI8179IJQY](/sequence-files/IGVFFI8179IJQY/), [IGVFFI5704YDAS](/sequence-files/IGVFFI5704YDAS/), [IGVFFI8791DZLT](/sequence-files/IGVFFI8791DZLT/), [IGVFFI9060TEPJ](/sequence-files/IGVFFI9060TEPJ/), [IGVFFI2286OUGE](/sequence-files/IGVFFI2286OUGE/), [IGVFFI7565AYPY](/sequence-files/IGVFFI7565AYPY/), [IGVFFI2481MCCR](/sequence-files/IGVFFI2481MCCR/), [IGVFFI9818ATKY](/sequence-files/IGVFFI9818ATKY/), [IGVFFI3526AJGW](/sequence-files/IGVFFI3526AJGW/), [IGVFFI1460NVPD](/sequence-files/IGVFFI1460NVPD/), [IGVFFI3171QMAV](/sequence-files/IGVFFI3171QMAV/), [IGVFFI3646VDRH](/sequence-files/IGVFFI3646VDRH/), [IGVFFI2530DOWL](/sequence-files/IGVFFI2530DOWL/), [IGVFFI1147YMVO](/sequence-files/IGVFFI1147YMVO/), [IGVFFI1285NAVD](/sequence-files/IGVFFI1285NAVD/), [IGVFFI8613NGOX](/sequence-files/IGVFFI8613NGOX/), [IGVFFI4439ZRPF](/sequence-files/IGVFFI4439ZRPF/), [IGVFFI2502PQTT](/sequence-files/IGVFFI2502PQTT/), [IGVFFI3866CQCZ](/sequence-files/IGVFFI3866CQCZ/), [IGVFFI1729TWDJ](/sequence-files/IGVFFI1729TWDJ/), [IGVFFI3236YFOB](/sequence-files/IGVFFI3236YFOB/), [IGVFFI0712MUJQ](/sequence-files/IGVFFI0712MUJQ/), [IGVFFI2963MBAS](/sequence-files/IGVFFI2963MBAS/), [IGVFFI7669EBVR](/sequence-files/IGVFFI7669EBVR/), [IGVFFI5837LENW](/sequence-files/IGVFFI5837LENW/), [IGVFFI2301YQZS](/sequence-files/IGVFFI2301YQZS/), [IGVFFI8889KEBC](/sequence-files/IGVFFI8889KEBC/), [IGVFFI3426OXDA](/sequence-files/IGVFFI3426OXDA/), [IGVFFI5424RVVH](/sequence-files/IGVFFI5424RVVH/), [IGVFFI9438WOHM](/sequence-files/IGVFFI9438WOHM/), [IGVFFI6175ELGI](/sequence-files/IGVFFI6175ELGI/), [IGVFFI4465XITE](/sequence-files/IGVFFI4465XITE/), [IGVFFI3688DSAI](/sequence-files/IGVFFI3688DSAI/), [IGVFFI8146DRHM](/sequence-files/IGVFFI8146DRHM/), [IGVFFI8746MPBC](/sequence-files/IGVFFI8746MPBC/), [IGVFFI7677QSPY](/sequence-files/IGVFFI7677QSPY/), [IGVFFI0962CKYZ](/sequence-files/IGVFFI0962CKYZ/), [IGVFFI4155RDZO](/sequence-files/IGVFFI4155RDZO/), [IGVFFI4977KIKA](/sequence-files/IGVFFI4977KIKA/), [IGVFFI7483ALXE](/sequence-files/IGVFFI7483ALXE/), [IGVFFI0864YVWT](/sequence-files/IGVFFI0864YVWT/), [IGVFFI7505YFRV](/sequence-files/IGVFFI7505YFRV/) 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/IGVFDS0791ADVW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0791ADVW](/auxiliary-sets/IGVFDS0791ADVW/) has sequence file(s) [IGVFFI8269CZGN](/sequence-files/IGVFFI8269CZGN/), [IGVFFI5970VSBC](/sequence-files/IGVFFI5970VSBC/), [IGVFFI5277SPHD](/sequence-files/IGVFFI5277SPHD/), [IGVFFI7239KLVT](/sequence-files/IGVFFI7239KLVT/), [IGVFFI4629NALN](/sequence-files/IGVFFI4629NALN/), [IGVFFI5202JJWF](/sequence-files/IGVFFI5202JJWF/), [IGVFFI8179IJQY](/sequence-files/IGVFFI8179IJQY/), [IGVFFI5704YDAS](/sequence-files/IGVFFI5704YDAS/), [IGVFFI8791DZLT](/sequence-files/IGVFFI8791DZLT/), [IGVFFI9060TEPJ](/sequence-files/IGVFFI9060TEPJ/), [IGVFFI2286OUGE](/sequence-files/IGVFFI2286OUGE/), [IGVFFI7565AYPY](/sequence-files/IGVFFI7565AYPY/), [IGVFFI2481MCCR](/sequence-files/IGVFFI2481MCCR/), [IGVFFI9818ATKY](/sequence-files/IGVFFI9818ATKY/), [IGVFFI3526AJGW](/sequence-files/IGVFFI3526AJGW/), [IGVFFI1460NVPD](/sequence-files/IGVFFI1460NVPD/), [IGVFFI3171QMAV](/sequence-files/IGVFFI3171QMAV/), [IGVFFI3646VDRH](/sequence-files/IGVFFI3646VDRH/), [IGVFFI2530DOWL](/sequence-files/IGVFFI2530DOWL/), [IGVFFI1147YMVO](/sequence-files/IGVFFI1147YMVO/), [IGVFFI1285NAVD](/sequence-files/IGVFFI1285NAVD/), [IGVFFI8613NGOX](/sequence-files/IGVFFI8613NGOX/), [IGVFFI4439ZRPF](/sequence-files/IGVFFI4439ZRPF/), [IGVFFI2502PQTT](/sequence-files/IGVFFI2502PQTT/), [IGVFFI3866CQCZ](/sequence-files/IGVFFI3866CQCZ/), [IGVFFI1729TWDJ](/sequence-files/IGVFFI1729TWDJ/), [IGVFFI3236YFOB](/sequence-files/IGVFFI3236YFOB/), [IGVFFI0712MUJQ](/sequence-files/IGVFFI0712MUJQ/), [IGVFFI2963MBAS](/sequence-files/IGVFFI2963MBAS/), [IGVFFI7669EBVR](/sequence-files/IGVFFI7669EBVR/), [IGVFFI5837LENW](/sequence-files/IGVFFI5837LENW/), [IGVFFI2301YQZS](/sequence-files/IGVFFI2301YQZS/), [IGVFFI8889KEBC](/sequence-files/IGVFFI8889KEBC/), [IGVFFI3426OXDA](/sequence-files/IGVFFI3426OXDA/), [IGVFFI5424RVVH](/sequence-files/IGVFFI5424RVVH/), [IGVFFI9438WOHM](/sequence-files/IGVFFI9438WOHM/), [IGVFFI6175ELGI](/sequence-files/IGVFFI6175ELGI/), [IGVFFI4465XITE](/sequence-files/IGVFFI4465XITE/), [IGVFFI3688DSAI](/sequence-files/IGVFFI3688DSAI/), [IGVFFI8146DRHM](/sequence-files/IGVFFI8146DRHM/), [IGVFFI8746MPBC](/sequence-files/IGVFFI8746MPBC/), [IGVFFI7677QSPY](/sequence-files/IGVFFI7677QSPY/), [IGVFFI0962CKYZ](/sequence-files/IGVFFI0962CKYZ/), [IGVFFI4155RDZO](/sequence-files/IGVFFI4155RDZO/), [IGVFFI4977KIKA](/sequence-files/IGVFFI4977KIKA/), [IGVFFI7483ALXE](/sequence-files/IGVFFI7483ALXE/), [IGVFFI0864YVWT](/sequence-files/IGVFFI0864YVWT/), [IGVFFI7505YFRV](/sequence-files/IGVFFI7505YFRV/) 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/IGVFDS0791ADVW/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0791ADVW](/auxiliary-sets/IGVFDS0791ADVW/) 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/IGVFDS0791ADVW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0791ADVW/",
"accession": "IGVFDS0791ADVW",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-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": "2023-12-01T00:05:33.574383+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": "2023-12-20T23:06:14.786109+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7954ICIY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7954ICIY",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-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": "2023-12-05T19:37:00.623312+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": "a9c2885f-658e-4a77-bb45-39922aa5fa1d"
}