{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2708HTXW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2708HTXW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-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 [IGVFSM8646DYNI](/in-vitro-systems/IGVFSM8646DYNI/) 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/IGVFSM8646DYNI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2708HTXW](/measurement-sets/IGVFDS2708HTXW/) has in progress subobject auxiliary set [IGVFDS2590KUJX](/auxiliary-sets/IGVFDS2590KUJX/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2708HTXW/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2708HTXW](/measurement-sets/IGVFDS2708HTXW/) 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/IGVFDS2708HTXW/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2590KUJX](/auxiliary-sets/IGVFDS2590KUJX/) has sequence file(s) [IGVFFI9357HYYG](/sequence-files/IGVFFI9357HYYG/), [IGVFFI6551FBMJ](/sequence-files/IGVFFI6551FBMJ/), [IGVFFI0327VZDN](/sequence-files/IGVFFI0327VZDN/), [IGVFFI5892UBRB](/sequence-files/IGVFFI5892UBRB/), [IGVFFI0178FLZC](/sequence-files/IGVFFI0178FLZC/), [IGVFFI0110IBGN](/sequence-files/IGVFFI0110IBGN/), [IGVFFI8318HDEK](/sequence-files/IGVFFI8318HDEK/), [IGVFFI4974TAPY](/sequence-files/IGVFFI4974TAPY/), [IGVFFI2522ZZGZ](/sequence-files/IGVFFI2522ZZGZ/), [IGVFFI4666JPYV](/sequence-files/IGVFFI4666JPYV/), [IGVFFI4469XSVM](/sequence-files/IGVFFI4469XSVM/), [IGVFFI0943QPRC](/sequence-files/IGVFFI0943QPRC/), [IGVFFI6094CBUA](/sequence-files/IGVFFI6094CBUA/), [IGVFFI5856FKXC](/sequence-files/IGVFFI5856FKXC/), [IGVFFI7173EUOZ](/sequence-files/IGVFFI7173EUOZ/), [IGVFFI3132GSET](/sequence-files/IGVFFI3132GSET/), [IGVFFI9351WCDC](/sequence-files/IGVFFI9351WCDC/), [IGVFFI0805UTCV](/sequence-files/IGVFFI0805UTCV/), [IGVFFI9139SKNU](/sequence-files/IGVFFI9139SKNU/), [IGVFFI4348YOVA](/sequence-files/IGVFFI4348YOVA/), [IGVFFI9726SQFG](/sequence-files/IGVFFI9726SQFG/), [IGVFFI2296VPVS](/sequence-files/IGVFFI2296VPVS/), [IGVFFI5665PYZU](/sequence-files/IGVFFI5665PYZU/), [IGVFFI6083RUFQ](/sequence-files/IGVFFI6083RUFQ/), [IGVFFI6067FVTF](/sequence-files/IGVFFI6067FVTF/), [IGVFFI6580BZXY](/sequence-files/IGVFFI6580BZXY/), [IGVFFI6843HAJB](/sequence-files/IGVFFI6843HAJB/), [IGVFFI3859FMIK](/sequence-files/IGVFFI3859FMIK/), [IGVFFI8381CFTB](/sequence-files/IGVFFI8381CFTB/), [IGVFFI6664FKEZ](/sequence-files/IGVFFI6664FKEZ/), [IGVFFI3681NZAE](/sequence-files/IGVFFI3681NZAE/), [IGVFFI9589TCDE](/sequence-files/IGVFFI9589TCDE/), [IGVFFI3918NSAB](/sequence-files/IGVFFI3918NSAB/), [IGVFFI3750RLHU](/sequence-files/IGVFFI3750RLHU/), [IGVFFI9493PKXZ](/sequence-files/IGVFFI9493PKXZ/), [IGVFFI4197ZIYF](/sequence-files/IGVFFI4197ZIYF/), [IGVFFI7693ARCI](/sequence-files/IGVFFI7693ARCI/), [IGVFFI8734SUDB](/sequence-files/IGVFFI8734SUDB/), [IGVFFI6515THLX](/sequence-files/IGVFFI6515THLX/), [IGVFFI3487EAVL](/sequence-files/IGVFFI3487EAVL/), [IGVFFI4810XFLN](/sequence-files/IGVFFI4810XFLN/), [IGVFFI9140DDRI](/sequence-files/IGVFFI9140DDRI/), [IGVFFI2369QLGT](/sequence-files/IGVFFI2369QLGT/), [IGVFFI1229MEEA](/sequence-files/IGVFFI1229MEEA/), [IGVFFI1071JIIN](/sequence-files/IGVFFI1071JIIN/), [IGVFFI6350BRHA](/sequence-files/IGVFFI6350BRHA/), [IGVFFI7346YTFK](/sequence-files/IGVFFI7346YTFK/), [IGVFFI7702NESZ](/sequence-files/IGVFFI7702NESZ/) 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/IGVFDS2590KUJX/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2590KUJX](/auxiliary-sets/IGVFDS2590KUJX/) has sequence file(s): [IGVFFI9357HYYG](/sequence-files/IGVFFI9357HYYG/), [IGVFFI6551FBMJ](/sequence-files/IGVFFI6551FBMJ/), [IGVFFI0327VZDN](/sequence-files/IGVFFI0327VZDN/), [IGVFFI5892UBRB](/sequence-files/IGVFFI5892UBRB/), [IGVFFI0178FLZC](/sequence-files/IGVFFI0178FLZC/), [IGVFFI0110IBGN](/sequence-files/IGVFFI0110IBGN/), [IGVFFI8318HDEK](/sequence-files/IGVFFI8318HDEK/), [IGVFFI4974TAPY](/sequence-files/IGVFFI4974TAPY/), [IGVFFI2522ZZGZ](/sequence-files/IGVFFI2522ZZGZ/), [IGVFFI4666JPYV](/sequence-files/IGVFFI4666JPYV/), [IGVFFI4469XSVM](/sequence-files/IGVFFI4469XSVM/), [IGVFFI0943QPRC](/sequence-files/IGVFFI0943QPRC/), [IGVFFI6094CBUA](/sequence-files/IGVFFI6094CBUA/), [IGVFFI5856FKXC](/sequence-files/IGVFFI5856FKXC/), [IGVFFI7173EUOZ](/sequence-files/IGVFFI7173EUOZ/), [IGVFFI3132GSET](/sequence-files/IGVFFI3132GSET/), [IGVFFI9351WCDC](/sequence-files/IGVFFI9351WCDC/), [IGVFFI0805UTCV](/sequence-files/IGVFFI0805UTCV/), [IGVFFI9139SKNU](/sequence-files/IGVFFI9139SKNU/), [IGVFFI4348YOVA](/sequence-files/IGVFFI4348YOVA/), [IGVFFI9726SQFG](/sequence-files/IGVFFI9726SQFG/), [IGVFFI2296VPVS](/sequence-files/IGVFFI2296VPVS/), [IGVFFI5665PYZU](/sequence-files/IGVFFI5665PYZU/), [IGVFFI6083RUFQ](/sequence-files/IGVFFI6083RUFQ/), [IGVFFI6067FVTF](/sequence-files/IGVFFI6067FVTF/), [IGVFFI6580BZXY](/sequence-files/IGVFFI6580BZXY/), [IGVFFI6843HAJB](/sequence-files/IGVFFI6843HAJB/), [IGVFFI3859FMIK](/sequence-files/IGVFFI3859FMIK/), [IGVFFI8381CFTB](/sequence-files/IGVFFI8381CFTB/), [IGVFFI6664FKEZ](/sequence-files/IGVFFI6664FKEZ/), [IGVFFI3681NZAE](/sequence-files/IGVFFI3681NZAE/), [IGVFFI9589TCDE](/sequence-files/IGVFFI9589TCDE/), [IGVFFI3918NSAB](/sequence-files/IGVFFI3918NSAB/), [IGVFFI3750RLHU](/sequence-files/IGVFFI3750RLHU/), [IGVFFI9493PKXZ](/sequence-files/IGVFFI9493PKXZ/), [IGVFFI4197ZIYF](/sequence-files/IGVFFI4197ZIYF/), [IGVFFI7693ARCI](/sequence-files/IGVFFI7693ARCI/), [IGVFFI8734SUDB](/sequence-files/IGVFFI8734SUDB/), [IGVFFI6515THLX](/sequence-files/IGVFFI6515THLX/), [IGVFFI3487EAVL](/sequence-files/IGVFFI3487EAVL/), [IGVFFI4810XFLN](/sequence-files/IGVFFI4810XFLN/), [IGVFFI9140DDRI](/sequence-files/IGVFFI9140DDRI/), [IGVFFI2369QLGT](/sequence-files/IGVFFI2369QLGT/), [IGVFFI1229MEEA](/sequence-files/IGVFFI1229MEEA/), [IGVFFI1071JIIN](/sequence-files/IGVFFI1071JIIN/), [IGVFFI6350BRHA](/sequence-files/IGVFFI6350BRHA/), [IGVFFI7346YTFK](/sequence-files/IGVFFI7346YTFK/), [IGVFFI7702NESZ](/sequence-files/IGVFFI7702NESZ/) 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/IGVFDS2590KUJX/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2590KUJX](/auxiliary-sets/IGVFDS2590KUJX/) 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_for",
"path": "/auxiliary-sets/IGVFDS2590KUJX/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2590KUJX/",
"accession": "IGVFDS2590KUJX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-01T00:04:41.209969+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_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": "2023-12-20T23:07:02.948529+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8646DYNI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8646DYNI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA"
],
"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 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected 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": "2023-12-05T19:09:11.234578+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": "eaf2c3f2-0680-4c53-a3b2-5974796b9258"
}