{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5405RYGU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5405RYGU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD_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 [IGVFDS5405RYGU](/measurement-sets/IGVFDS5405RYGU/) has in progress subobject auxiliary set [IGVFDS7701USEL](/auxiliary-sets/IGVFDS7701USEL/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5405RYGU/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6331RKYX](/in-vitro-systems/IGVFSM6331RKYX/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6331RKYX/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5405RYGU](/measurement-sets/IGVFDS5405RYGU/) 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/IGVFDS5405RYGU/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7701USEL](/auxiliary-sets/IGVFDS7701USEL/) has sequence file(s) [IGVFFI0898KSJR](/sequence-files/IGVFFI0898KSJR/), [IGVFFI8602XCBR](/sequence-files/IGVFFI8602XCBR/), [IGVFFI8179KVKI](/sequence-files/IGVFFI8179KVKI/), [IGVFFI3437WHNQ](/sequence-files/IGVFFI3437WHNQ/), [IGVFFI3614BVAY](/sequence-files/IGVFFI3614BVAY/), [IGVFFI0267EBZW](/sequence-files/IGVFFI0267EBZW/), [IGVFFI6214KLPO](/sequence-files/IGVFFI6214KLPO/), [IGVFFI6493OGUO](/sequence-files/IGVFFI6493OGUO/), [IGVFFI3667ASMR](/sequence-files/IGVFFI3667ASMR/), [IGVFFI6879VNXZ](/sequence-files/IGVFFI6879VNXZ/), [IGVFFI9085EHXI](/sequence-files/IGVFFI9085EHXI/), [IGVFFI4292LYJU](/sequence-files/IGVFFI4292LYJU/), [IGVFFI0553UBWG](/sequence-files/IGVFFI0553UBWG/), [IGVFFI5920LYEU](/sequence-files/IGVFFI5920LYEU/), [IGVFFI8573LNOD](/sequence-files/IGVFFI8573LNOD/), [IGVFFI4636QHGS](/sequence-files/IGVFFI4636QHGS/), [IGVFFI6684RYQW](/sequence-files/IGVFFI6684RYQW/), [IGVFFI6094UFWL](/sequence-files/IGVFFI6094UFWL/), [IGVFFI3742YENH](/sequence-files/IGVFFI3742YENH/), [IGVFFI1287CKNT](/sequence-files/IGVFFI1287CKNT/), [IGVFFI7579EAPB](/sequence-files/IGVFFI7579EAPB/), [IGVFFI5361ZAGU](/sequence-files/IGVFFI5361ZAGU/), [IGVFFI0583XHMV](/sequence-files/IGVFFI0583XHMV/), [IGVFFI4748HJGK](/sequence-files/IGVFFI4748HJGK/), [IGVFFI2792QYHQ](/sequence-files/IGVFFI2792QYHQ/), [IGVFFI5849LHNQ](/sequence-files/IGVFFI5849LHNQ/), [IGVFFI8544SSHH](/sequence-files/IGVFFI8544SSHH/), [IGVFFI3849YHMD](/sequence-files/IGVFFI3849YHMD/), [IGVFFI6351LQJK](/sequence-files/IGVFFI6351LQJK/), [IGVFFI4425ZZGW](/sequence-files/IGVFFI4425ZZGW/), [IGVFFI4509QWNW](/sequence-files/IGVFFI4509QWNW/), [IGVFFI4189OREP](/sequence-files/IGVFFI4189OREP/), [IGVFFI1854KRJY](/sequence-files/IGVFFI1854KRJY/), [IGVFFI8799ZDJS](/sequence-files/IGVFFI8799ZDJS/), [IGVFFI5084POXE](/sequence-files/IGVFFI5084POXE/), [IGVFFI8687AKIE](/sequence-files/IGVFFI8687AKIE/), [IGVFFI3611YEOE](/sequence-files/IGVFFI3611YEOE/), [IGVFFI1769RTVV](/sequence-files/IGVFFI1769RTVV/), [IGVFFI1887INXT](/sequence-files/IGVFFI1887INXT/), [IGVFFI0219LPMU](/sequence-files/IGVFFI0219LPMU/), [IGVFFI9793IGUJ](/sequence-files/IGVFFI9793IGUJ/), [IGVFFI6588TAXD](/sequence-files/IGVFFI6588TAXD/), [IGVFFI1958UOUF](/sequence-files/IGVFFI1958UOUF/), [IGVFFI7003KKNC](/sequence-files/IGVFFI7003KKNC/), [IGVFFI3408LAGR](/sequence-files/IGVFFI3408LAGR/), [IGVFFI2981MOWH](/sequence-files/IGVFFI2981MOWH/), [IGVFFI7973WACJ](/sequence-files/IGVFFI7973WACJ/), [IGVFFI5865YWJA](/sequence-files/IGVFFI5865YWJA/) 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/IGVFDS7701USEL/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7701USEL](/auxiliary-sets/IGVFDS7701USEL/) has sequence file(s): [IGVFFI0898KSJR](/sequence-files/IGVFFI0898KSJR/), [IGVFFI8602XCBR](/sequence-files/IGVFFI8602XCBR/), [IGVFFI8179KVKI](/sequence-files/IGVFFI8179KVKI/), [IGVFFI3437WHNQ](/sequence-files/IGVFFI3437WHNQ/), [IGVFFI3614BVAY](/sequence-files/IGVFFI3614BVAY/), [IGVFFI0267EBZW](/sequence-files/IGVFFI0267EBZW/), [IGVFFI6214KLPO](/sequence-files/IGVFFI6214KLPO/), [IGVFFI6493OGUO](/sequence-files/IGVFFI6493OGUO/), [IGVFFI3667ASMR](/sequence-files/IGVFFI3667ASMR/), [IGVFFI6879VNXZ](/sequence-files/IGVFFI6879VNXZ/), [IGVFFI9085EHXI](/sequence-files/IGVFFI9085EHXI/), [IGVFFI4292LYJU](/sequence-files/IGVFFI4292LYJU/), [IGVFFI0553UBWG](/sequence-files/IGVFFI0553UBWG/), [IGVFFI5920LYEU](/sequence-files/IGVFFI5920LYEU/), [IGVFFI8573LNOD](/sequence-files/IGVFFI8573LNOD/), [IGVFFI4636QHGS](/sequence-files/IGVFFI4636QHGS/), [IGVFFI6684RYQW](/sequence-files/IGVFFI6684RYQW/), [IGVFFI6094UFWL](/sequence-files/IGVFFI6094UFWL/), [IGVFFI3742YENH](/sequence-files/IGVFFI3742YENH/), [IGVFFI1287CKNT](/sequence-files/IGVFFI1287CKNT/), [IGVFFI7579EAPB](/sequence-files/IGVFFI7579EAPB/), [IGVFFI5361ZAGU](/sequence-files/IGVFFI5361ZAGU/), [IGVFFI0583XHMV](/sequence-files/IGVFFI0583XHMV/), [IGVFFI4748HJGK](/sequence-files/IGVFFI4748HJGK/), [IGVFFI2792QYHQ](/sequence-files/IGVFFI2792QYHQ/), [IGVFFI5849LHNQ](/sequence-files/IGVFFI5849LHNQ/), [IGVFFI8544SSHH](/sequence-files/IGVFFI8544SSHH/), [IGVFFI3849YHMD](/sequence-files/IGVFFI3849YHMD/), [IGVFFI6351LQJK](/sequence-files/IGVFFI6351LQJK/), [IGVFFI4425ZZGW](/sequence-files/IGVFFI4425ZZGW/), [IGVFFI4509QWNW](/sequence-files/IGVFFI4509QWNW/), [IGVFFI4189OREP](/sequence-files/IGVFFI4189OREP/), [IGVFFI1854KRJY](/sequence-files/IGVFFI1854KRJY/), [IGVFFI8799ZDJS](/sequence-files/IGVFFI8799ZDJS/), [IGVFFI5084POXE](/sequence-files/IGVFFI5084POXE/), [IGVFFI8687AKIE](/sequence-files/IGVFFI8687AKIE/), [IGVFFI3611YEOE](/sequence-files/IGVFFI3611YEOE/), [IGVFFI1769RTVV](/sequence-files/IGVFFI1769RTVV/), [IGVFFI1887INXT](/sequence-files/IGVFFI1887INXT/), [IGVFFI0219LPMU](/sequence-files/IGVFFI0219LPMU/), [IGVFFI9793IGUJ](/sequence-files/IGVFFI9793IGUJ/), [IGVFFI6588TAXD](/sequence-files/IGVFFI6588TAXD/), [IGVFFI1958UOUF](/sequence-files/IGVFFI1958UOUF/), [IGVFFI7003KKNC](/sequence-files/IGVFFI7003KKNC/), [IGVFFI3408LAGR](/sequence-files/IGVFFI3408LAGR/), [IGVFFI2981MOWH](/sequence-files/IGVFFI2981MOWH/), [IGVFFI7973WACJ](/sequence-files/IGVFFI7973WACJ/), [IGVFFI5865YWJA](/sequence-files/IGVFFI5865YWJA/) 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/IGVFDS7701USEL/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7701USEL](/auxiliary-sets/IGVFDS7701USEL/) 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/IGVFDS7701USEL/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7701USEL/",
"accession": "IGVFDS7701USEL",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD_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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-01T00:04:45.584078+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/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": "2023-12-20T23:05:42.845014+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6331RKYX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6331RKYX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"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 76-100% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:33:06.388762+00:00",
"summary": "prime editing 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": "f016c775-b215-4660-b119-5a7f3b736144"
}