{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0872DEIB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0872DEIB",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-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 in vitro system [IGVFSM3467IDCX](/in-vitro-systems/IGVFSM3467IDCX/) 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/IGVFSM3467IDCX/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0872DEIB](/measurement-sets/IGVFDS0872DEIB/) has in progress subobject auxiliary set [IGVFDS3725JSYO](/auxiliary-sets/IGVFDS3725JSYO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0872DEIB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0872DEIB](/measurement-sets/IGVFDS0872DEIB/) 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/IGVFDS0872DEIB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3725JSYO](/auxiliary-sets/IGVFDS3725JSYO/) has sequence file(s): [IGVFFI8638TCGO](/sequence-files/IGVFFI8638TCGO/), [IGVFFI8109NITQ](/sequence-files/IGVFFI8109NITQ/), [IGVFFI6179XXDH](/sequence-files/IGVFFI6179XXDH/), [IGVFFI8154AJMP](/sequence-files/IGVFFI8154AJMP/), [IGVFFI6331ZPTC](/sequence-files/IGVFFI6331ZPTC/), [IGVFFI8845PCNO](/sequence-files/IGVFFI8845PCNO/), [IGVFFI1935JILX](/sequence-files/IGVFFI1935JILX/), [IGVFFI8405HCME](/sequence-files/IGVFFI8405HCME/), [IGVFFI1643LYMG](/sequence-files/IGVFFI1643LYMG/), [IGVFFI2910QBII](/sequence-files/IGVFFI2910QBII/), [IGVFFI9235CGPE](/sequence-files/IGVFFI9235CGPE/), [IGVFFI4573JFJK](/sequence-files/IGVFFI4573JFJK/), [IGVFFI5635KDID](/sequence-files/IGVFFI5635KDID/), [IGVFFI1498BTSR](/sequence-files/IGVFFI1498BTSR/), [IGVFFI4865ONEK](/sequence-files/IGVFFI4865ONEK/), [IGVFFI4878XBGB](/sequence-files/IGVFFI4878XBGB/), [IGVFFI3300WBZW](/sequence-files/IGVFFI3300WBZW/), [IGVFFI6115MGMH](/sequence-files/IGVFFI6115MGMH/), [IGVFFI5930RGWG](/sequence-files/IGVFFI5930RGWG/), [IGVFFI1153KKCP](/sequence-files/IGVFFI1153KKCP/), [IGVFFI3794NDKE](/sequence-files/IGVFFI3794NDKE/), [IGVFFI2205IBWF](/sequence-files/IGVFFI2205IBWF/), [IGVFFI2118MSMM](/sequence-files/IGVFFI2118MSMM/), [IGVFFI4277VILJ](/sequence-files/IGVFFI4277VILJ/), [IGVFFI4740KBSJ](/sequence-files/IGVFFI4740KBSJ/), [IGVFFI0566ZKCN](/sequence-files/IGVFFI0566ZKCN/), [IGVFFI6506GWDI](/sequence-files/IGVFFI6506GWDI/), [IGVFFI5741VODP](/sequence-files/IGVFFI5741VODP/), [IGVFFI1990CBJX](/sequence-files/IGVFFI1990CBJX/), [IGVFFI4145AAJP](/sequence-files/IGVFFI4145AAJP/), [IGVFFI3958ZOYE](/sequence-files/IGVFFI3958ZOYE/), [IGVFFI6873RNCJ](/sequence-files/IGVFFI6873RNCJ/), [IGVFFI8396KMOX](/sequence-files/IGVFFI8396KMOX/), [IGVFFI9948XQHH](/sequence-files/IGVFFI9948XQHH/), [IGVFFI6717RCWI](/sequence-files/IGVFFI6717RCWI/), [IGVFFI7525AUIK](/sequence-files/IGVFFI7525AUIK/), [IGVFFI4639IDVU](/sequence-files/IGVFFI4639IDVU/), [IGVFFI9558SOFB](/sequence-files/IGVFFI9558SOFB/), [IGVFFI6581DRVN](/sequence-files/IGVFFI6581DRVN/), [IGVFFI1668TYGS](/sequence-files/IGVFFI1668TYGS/), [IGVFFI4471BFBY](/sequence-files/IGVFFI4471BFBY/), [IGVFFI3049LEUK](/sequence-files/IGVFFI3049LEUK/), [IGVFFI0708IVTV](/sequence-files/IGVFFI0708IVTV/), [IGVFFI6601UNIT](/sequence-files/IGVFFI6601UNIT/), [IGVFFI8754HTDA](/sequence-files/IGVFFI8754HTDA/), [IGVFFI3878REHP](/sequence-files/IGVFFI3878REHP/), [IGVFFI2554SDYO](/sequence-files/IGVFFI2554SDYO/), [IGVFFI4420AJWD](/sequence-files/IGVFFI4420AJWD/) 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/IGVFDS3725JSYO/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3725JSYO](/auxiliary-sets/IGVFDS3725JSYO/) has sequence file(s) [IGVFFI8638TCGO](/sequence-files/IGVFFI8638TCGO/), [IGVFFI8109NITQ](/sequence-files/IGVFFI8109NITQ/), [IGVFFI6179XXDH](/sequence-files/IGVFFI6179XXDH/), [IGVFFI8154AJMP](/sequence-files/IGVFFI8154AJMP/), [IGVFFI6331ZPTC](/sequence-files/IGVFFI6331ZPTC/), [IGVFFI8845PCNO](/sequence-files/IGVFFI8845PCNO/), [IGVFFI1935JILX](/sequence-files/IGVFFI1935JILX/), [IGVFFI8405HCME](/sequence-files/IGVFFI8405HCME/), [IGVFFI1643LYMG](/sequence-files/IGVFFI1643LYMG/), [IGVFFI2910QBII](/sequence-files/IGVFFI2910QBII/), [IGVFFI9235CGPE](/sequence-files/IGVFFI9235CGPE/), [IGVFFI4573JFJK](/sequence-files/IGVFFI4573JFJK/), [IGVFFI5635KDID](/sequence-files/IGVFFI5635KDID/), [IGVFFI1498BTSR](/sequence-files/IGVFFI1498BTSR/), [IGVFFI4865ONEK](/sequence-files/IGVFFI4865ONEK/), [IGVFFI4878XBGB](/sequence-files/IGVFFI4878XBGB/), [IGVFFI3300WBZW](/sequence-files/IGVFFI3300WBZW/), [IGVFFI6115MGMH](/sequence-files/IGVFFI6115MGMH/), [IGVFFI5930RGWG](/sequence-files/IGVFFI5930RGWG/), [IGVFFI1153KKCP](/sequence-files/IGVFFI1153KKCP/), [IGVFFI3794NDKE](/sequence-files/IGVFFI3794NDKE/), [IGVFFI2205IBWF](/sequence-files/IGVFFI2205IBWF/), [IGVFFI2118MSMM](/sequence-files/IGVFFI2118MSMM/), [IGVFFI4277VILJ](/sequence-files/IGVFFI4277VILJ/), [IGVFFI4740KBSJ](/sequence-files/IGVFFI4740KBSJ/), [IGVFFI0566ZKCN](/sequence-files/IGVFFI0566ZKCN/), [IGVFFI6506GWDI](/sequence-files/IGVFFI6506GWDI/), [IGVFFI5741VODP](/sequence-files/IGVFFI5741VODP/), [IGVFFI1990CBJX](/sequence-files/IGVFFI1990CBJX/), [IGVFFI4145AAJP](/sequence-files/IGVFFI4145AAJP/), [IGVFFI3958ZOYE](/sequence-files/IGVFFI3958ZOYE/), [IGVFFI6873RNCJ](/sequence-files/IGVFFI6873RNCJ/), [IGVFFI8396KMOX](/sequence-files/IGVFFI8396KMOX/), [IGVFFI9948XQHH](/sequence-files/IGVFFI9948XQHH/), [IGVFFI6717RCWI](/sequence-files/IGVFFI6717RCWI/), [IGVFFI7525AUIK](/sequence-files/IGVFFI7525AUIK/), [IGVFFI4639IDVU](/sequence-files/IGVFFI4639IDVU/), [IGVFFI9558SOFB](/sequence-files/IGVFFI9558SOFB/), [IGVFFI6581DRVN](/sequence-files/IGVFFI6581DRVN/), [IGVFFI1668TYGS](/sequence-files/IGVFFI1668TYGS/), [IGVFFI4471BFBY](/sequence-files/IGVFFI4471BFBY/), [IGVFFI3049LEUK](/sequence-files/IGVFFI3049LEUK/), [IGVFFI0708IVTV](/sequence-files/IGVFFI0708IVTV/), [IGVFFI6601UNIT](/sequence-files/IGVFFI6601UNIT/), [IGVFFI8754HTDA](/sequence-files/IGVFFI8754HTDA/), [IGVFFI3878REHP](/sequence-files/IGVFFI3878REHP/), [IGVFFI2554SDYO](/sequence-files/IGVFFI2554SDYO/), [IGVFFI4420AJWD](/sequence-files/IGVFFI4420AJWD/) 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/IGVFDS3725JSYO/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3725JSYO](/auxiliary-sets/IGVFDS3725JSYO/) 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/IGVFDS3725JSYO/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3725JSYO/",
"accession": "IGVFDS3725JSYO",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:45.520450+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/IGVFDS4359OODY/"
],
"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": "2023-12-20T23:07:21.287662+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3467IDCX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3467IDCX",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC"
],
"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_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": "2023-12-13T08:59:00.350266+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": "8064e61f-7098-4f50-bf5b-db46f383702c"
}