{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0744DITV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0744DITV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinA_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 [IGVFSM4599PEWQ](/in-vitro-systems/IGVFSM4599PEWQ/) 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/IGVFSM4599PEWQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0744DITV](/measurement-sets/IGVFDS0744DITV/) has in progress subobject auxiliary set [IGVFDS2513JNDD](/auxiliary-sets/IGVFDS2513JNDD/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0744DITV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2513JNDD](/auxiliary-sets/IGVFDS2513JNDD/) has sequence file(s): [IGVFFI4964CBCT](/sequence-files/IGVFFI4964CBCT/), [IGVFFI0886WXJY](/sequence-files/IGVFFI0886WXJY/), [IGVFFI1018EVZI](/sequence-files/IGVFFI1018EVZI/), [IGVFFI1073ZSLH](/sequence-files/IGVFFI1073ZSLH/), [IGVFFI3142XCZJ](/sequence-files/IGVFFI3142XCZJ/), [IGVFFI4297SGFU](/sequence-files/IGVFFI4297SGFU/), [IGVFFI8191KQII](/sequence-files/IGVFFI8191KQII/), [IGVFFI8964OBGH](/sequence-files/IGVFFI8964OBGH/), [IGVFFI0194FZAD](/sequence-files/IGVFFI0194FZAD/), [IGVFFI3918QBBM](/sequence-files/IGVFFI3918QBBM/), [IGVFFI5796CPXD](/sequence-files/IGVFFI5796CPXD/), [IGVFFI8706DBCO](/sequence-files/IGVFFI8706DBCO/), [IGVFFI3028EYTI](/sequence-files/IGVFFI3028EYTI/), [IGVFFI1471BZKW](/sequence-files/IGVFFI1471BZKW/), [IGVFFI2073IQFY](/sequence-files/IGVFFI2073IQFY/), [IGVFFI9496ZQBS](/sequence-files/IGVFFI9496ZQBS/), [IGVFFI9425QVXR](/sequence-files/IGVFFI9425QVXR/), [IGVFFI2796NLDA](/sequence-files/IGVFFI2796NLDA/), [IGVFFI2577KSQG](/sequence-files/IGVFFI2577KSQG/), [IGVFFI3200EYFR](/sequence-files/IGVFFI3200EYFR/), [IGVFFI5036QMNI](/sequence-files/IGVFFI5036QMNI/), [IGVFFI7685STPO](/sequence-files/IGVFFI7685STPO/), [IGVFFI1479STKN](/sequence-files/IGVFFI1479STKN/), [IGVFFI8133SCWY](/sequence-files/IGVFFI8133SCWY/), [IGVFFI2791LYTA](/sequence-files/IGVFFI2791LYTA/), [IGVFFI7078JLCE](/sequence-files/IGVFFI7078JLCE/), [IGVFFI4063OSHO](/sequence-files/IGVFFI4063OSHO/), [IGVFFI5642VKXS](/sequence-files/IGVFFI5642VKXS/), [IGVFFI0481IKPP](/sequence-files/IGVFFI0481IKPP/), [IGVFFI5421RNOS](/sequence-files/IGVFFI5421RNOS/), [IGVFFI9727RMNQ](/sequence-files/IGVFFI9727RMNQ/), [IGVFFI8584ONBJ](/sequence-files/IGVFFI8584ONBJ/), [IGVFFI7326BLMW](/sequence-files/IGVFFI7326BLMW/), [IGVFFI2132TIXB](/sequence-files/IGVFFI2132TIXB/), [IGVFFI6687MPQG](/sequence-files/IGVFFI6687MPQG/), [IGVFFI9210NPAI](/sequence-files/IGVFFI9210NPAI/), [IGVFFI2504QRRC](/sequence-files/IGVFFI2504QRRC/), [IGVFFI5575EGRW](/sequence-files/IGVFFI5575EGRW/), [IGVFFI3324QJXL](/sequence-files/IGVFFI3324QJXL/), [IGVFFI1796QDGJ](/sequence-files/IGVFFI1796QDGJ/), [IGVFFI7832NMCV](/sequence-files/IGVFFI7832NMCV/), [IGVFFI2721CXVA](/sequence-files/IGVFFI2721CXVA/), [IGVFFI1007LTEP](/sequence-files/IGVFFI1007LTEP/), [IGVFFI2621HAXU](/sequence-files/IGVFFI2621HAXU/), [IGVFFI4332KSVL](/sequence-files/IGVFFI4332KSVL/), [IGVFFI4689TRNY](/sequence-files/IGVFFI4689TRNY/), [IGVFFI3136MTFR](/sequence-files/IGVFFI3136MTFR/), [IGVFFI4886QLWI](/sequence-files/IGVFFI4886QLWI/) 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/IGVFDS2513JNDD/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0744DITV](/measurement-sets/IGVFDS0744DITV/) 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/IGVFDS0744DITV/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2513JNDD](/auxiliary-sets/IGVFDS2513JNDD/) has sequence file(s) [IGVFFI4964CBCT](/sequence-files/IGVFFI4964CBCT/), [IGVFFI0886WXJY](/sequence-files/IGVFFI0886WXJY/), [IGVFFI1018EVZI](/sequence-files/IGVFFI1018EVZI/), [IGVFFI1073ZSLH](/sequence-files/IGVFFI1073ZSLH/), [IGVFFI3142XCZJ](/sequence-files/IGVFFI3142XCZJ/), [IGVFFI4297SGFU](/sequence-files/IGVFFI4297SGFU/), [IGVFFI8191KQII](/sequence-files/IGVFFI8191KQII/), [IGVFFI8964OBGH](/sequence-files/IGVFFI8964OBGH/), [IGVFFI0194FZAD](/sequence-files/IGVFFI0194FZAD/), [IGVFFI3918QBBM](/sequence-files/IGVFFI3918QBBM/), [IGVFFI5796CPXD](/sequence-files/IGVFFI5796CPXD/), [IGVFFI8706DBCO](/sequence-files/IGVFFI8706DBCO/), [IGVFFI3028EYTI](/sequence-files/IGVFFI3028EYTI/), [IGVFFI1471BZKW](/sequence-files/IGVFFI1471BZKW/), [IGVFFI2073IQFY](/sequence-files/IGVFFI2073IQFY/), [IGVFFI9496ZQBS](/sequence-files/IGVFFI9496ZQBS/), [IGVFFI9425QVXR](/sequence-files/IGVFFI9425QVXR/), [IGVFFI2796NLDA](/sequence-files/IGVFFI2796NLDA/), [IGVFFI2577KSQG](/sequence-files/IGVFFI2577KSQG/), [IGVFFI3200EYFR](/sequence-files/IGVFFI3200EYFR/), [IGVFFI5036QMNI](/sequence-files/IGVFFI5036QMNI/), [IGVFFI7685STPO](/sequence-files/IGVFFI7685STPO/), [IGVFFI1479STKN](/sequence-files/IGVFFI1479STKN/), [IGVFFI8133SCWY](/sequence-files/IGVFFI8133SCWY/), [IGVFFI2791LYTA](/sequence-files/IGVFFI2791LYTA/), [IGVFFI7078JLCE](/sequence-files/IGVFFI7078JLCE/), [IGVFFI4063OSHO](/sequence-files/IGVFFI4063OSHO/), [IGVFFI5642VKXS](/sequence-files/IGVFFI5642VKXS/), [IGVFFI0481IKPP](/sequence-files/IGVFFI0481IKPP/), [IGVFFI5421RNOS](/sequence-files/IGVFFI5421RNOS/), [IGVFFI9727RMNQ](/sequence-files/IGVFFI9727RMNQ/), [IGVFFI8584ONBJ](/sequence-files/IGVFFI8584ONBJ/), [IGVFFI7326BLMW](/sequence-files/IGVFFI7326BLMW/), [IGVFFI2132TIXB](/sequence-files/IGVFFI2132TIXB/), [IGVFFI6687MPQG](/sequence-files/IGVFFI6687MPQG/), [IGVFFI9210NPAI](/sequence-files/IGVFFI9210NPAI/), [IGVFFI2504QRRC](/sequence-files/IGVFFI2504QRRC/), [IGVFFI5575EGRW](/sequence-files/IGVFFI5575EGRW/), [IGVFFI3324QJXL](/sequence-files/IGVFFI3324QJXL/), [IGVFFI1796QDGJ](/sequence-files/IGVFFI1796QDGJ/), [IGVFFI7832NMCV](/sequence-files/IGVFFI7832NMCV/), [IGVFFI2721CXVA](/sequence-files/IGVFFI2721CXVA/), [IGVFFI1007LTEP](/sequence-files/IGVFFI1007LTEP/), [IGVFFI2621HAXU](/sequence-files/IGVFFI2621HAXU/), [IGVFFI4332KSVL](/sequence-files/IGVFFI4332KSVL/), [IGVFFI4689TRNY](/sequence-files/IGVFFI4689TRNY/), [IGVFFI3136MTFR](/sequence-files/IGVFFI3136MTFR/), [IGVFFI4886QLWI](/sequence-files/IGVFFI4886QLWI/) 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/IGVFDS2513JNDD/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2513JNDD](/auxiliary-sets/IGVFDS2513JNDD/) 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/IGVFDS2513JNDD/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2513JNDD/",
"accession": "IGVFDS2513JNDD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinA_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": "2023-11-30T22:50:08.154338+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": "2023-12-20T23:06:26.337442+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4599PEWQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4599PEWQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinA"
],
"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 0-25% 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": "2023-12-05T22:57:43.967463+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": "a5b47e31-7e20-43e5-9664-ba4c7d387bb8"
}