{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3326NVFS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3326NVFS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-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 [IGVFDS3326NVFS](/measurement-sets/IGVFDS3326NVFS/) has in progress subobject auxiliary set [IGVFDS8040RMZU](/auxiliary-sets/IGVFDS8040RMZU/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3326NVFS/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6196LFWY](/in-vitro-systems/IGVFSM6196LFWY/) 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/IGVFSM6196LFWY/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3326NVFS](/measurement-sets/IGVFDS3326NVFS/) 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/IGVFDS3326NVFS/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8040RMZU](/auxiliary-sets/IGVFDS8040RMZU/) has sequence file(s): [IGVFFI8016NYWO](/sequence-files/IGVFFI8016NYWO/), [IGVFFI1444KQFJ](/sequence-files/IGVFFI1444KQFJ/), [IGVFFI5191TUWB](/sequence-files/IGVFFI5191TUWB/), [IGVFFI0123ADIP](/sequence-files/IGVFFI0123ADIP/), [IGVFFI6880CNHY](/sequence-files/IGVFFI6880CNHY/), [IGVFFI2617WVMQ](/sequence-files/IGVFFI2617WVMQ/), [IGVFFI8424PUCG](/sequence-files/IGVFFI8424PUCG/), [IGVFFI4073GXTM](/sequence-files/IGVFFI4073GXTM/), [IGVFFI7709LVDB](/sequence-files/IGVFFI7709LVDB/), [IGVFFI0867YMCU](/sequence-files/IGVFFI0867YMCU/), [IGVFFI8728QLKF](/sequence-files/IGVFFI8728QLKF/), [IGVFFI0246WLIS](/sequence-files/IGVFFI0246WLIS/), [IGVFFI8270XVGK](/sequence-files/IGVFFI8270XVGK/), [IGVFFI6608TLPQ](/sequence-files/IGVFFI6608TLPQ/), [IGVFFI0508OVBU](/sequence-files/IGVFFI0508OVBU/), [IGVFFI3437HYBR](/sequence-files/IGVFFI3437HYBR/), [IGVFFI5708BEHG](/sequence-files/IGVFFI5708BEHG/), [IGVFFI4407KUVD](/sequence-files/IGVFFI4407KUVD/), [IGVFFI9488LUIK](/sequence-files/IGVFFI9488LUIK/), [IGVFFI4548OMAK](/sequence-files/IGVFFI4548OMAK/), [IGVFFI9776OKNO](/sequence-files/IGVFFI9776OKNO/), [IGVFFI4798LOFZ](/sequence-files/IGVFFI4798LOFZ/), [IGVFFI3752GUAO](/sequence-files/IGVFFI3752GUAO/), [IGVFFI1088XKRT](/sequence-files/IGVFFI1088XKRT/), [IGVFFI8358IADX](/sequence-files/IGVFFI8358IADX/), [IGVFFI1082AMST](/sequence-files/IGVFFI1082AMST/), [IGVFFI5946KIFR](/sequence-files/IGVFFI5946KIFR/), [IGVFFI6211HFJI](/sequence-files/IGVFFI6211HFJI/), [IGVFFI4981QRBU](/sequence-files/IGVFFI4981QRBU/), [IGVFFI7831WEPE](/sequence-files/IGVFFI7831WEPE/), [IGVFFI9296JNYS](/sequence-files/IGVFFI9296JNYS/), [IGVFFI1277EBKM](/sequence-files/IGVFFI1277EBKM/), [IGVFFI2940UYKS](/sequence-files/IGVFFI2940UYKS/), [IGVFFI4062DZXY](/sequence-files/IGVFFI4062DZXY/), [IGVFFI6081UGVZ](/sequence-files/IGVFFI6081UGVZ/), [IGVFFI0134ACNG](/sequence-files/IGVFFI0134ACNG/), [IGVFFI9972QWZM](/sequence-files/IGVFFI9972QWZM/), [IGVFFI6937MHGN](/sequence-files/IGVFFI6937MHGN/), [IGVFFI1309XRYA](/sequence-files/IGVFFI1309XRYA/), [IGVFFI4261PVJC](/sequence-files/IGVFFI4261PVJC/), [IGVFFI7552MBTV](/sequence-files/IGVFFI7552MBTV/), [IGVFFI8012RRXD](/sequence-files/IGVFFI8012RRXD/), [IGVFFI6181NBYT](/sequence-files/IGVFFI6181NBYT/), [IGVFFI1064TWGN](/sequence-files/IGVFFI1064TWGN/), [IGVFFI0441JLWA](/sequence-files/IGVFFI0441JLWA/), [IGVFFI6813LUGK](/sequence-files/IGVFFI6813LUGK/), [IGVFFI7761WZTQ](/sequence-files/IGVFFI7761WZTQ/), [IGVFFI6849HRJB](/sequence-files/IGVFFI6849HRJB/) 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/IGVFDS8040RMZU/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8040RMZU](/auxiliary-sets/IGVFDS8040RMZU/) has sequence file(s) [IGVFFI8016NYWO](/sequence-files/IGVFFI8016NYWO/), [IGVFFI1444KQFJ](/sequence-files/IGVFFI1444KQFJ/), [IGVFFI5191TUWB](/sequence-files/IGVFFI5191TUWB/), [IGVFFI0123ADIP](/sequence-files/IGVFFI0123ADIP/), [IGVFFI6880CNHY](/sequence-files/IGVFFI6880CNHY/), [IGVFFI2617WVMQ](/sequence-files/IGVFFI2617WVMQ/), [IGVFFI8424PUCG](/sequence-files/IGVFFI8424PUCG/), [IGVFFI4073GXTM](/sequence-files/IGVFFI4073GXTM/), [IGVFFI7709LVDB](/sequence-files/IGVFFI7709LVDB/), [IGVFFI0867YMCU](/sequence-files/IGVFFI0867YMCU/), [IGVFFI8728QLKF](/sequence-files/IGVFFI8728QLKF/), [IGVFFI0246WLIS](/sequence-files/IGVFFI0246WLIS/), [IGVFFI8270XVGK](/sequence-files/IGVFFI8270XVGK/), [IGVFFI6608TLPQ](/sequence-files/IGVFFI6608TLPQ/), [IGVFFI0508OVBU](/sequence-files/IGVFFI0508OVBU/), [IGVFFI3437HYBR](/sequence-files/IGVFFI3437HYBR/), [IGVFFI5708BEHG](/sequence-files/IGVFFI5708BEHG/), [IGVFFI4407KUVD](/sequence-files/IGVFFI4407KUVD/), [IGVFFI9488LUIK](/sequence-files/IGVFFI9488LUIK/), [IGVFFI4548OMAK](/sequence-files/IGVFFI4548OMAK/), [IGVFFI9776OKNO](/sequence-files/IGVFFI9776OKNO/), [IGVFFI4798LOFZ](/sequence-files/IGVFFI4798LOFZ/), [IGVFFI3752GUAO](/sequence-files/IGVFFI3752GUAO/), [IGVFFI1088XKRT](/sequence-files/IGVFFI1088XKRT/), [IGVFFI8358IADX](/sequence-files/IGVFFI8358IADX/), [IGVFFI1082AMST](/sequence-files/IGVFFI1082AMST/), [IGVFFI5946KIFR](/sequence-files/IGVFFI5946KIFR/), [IGVFFI6211HFJI](/sequence-files/IGVFFI6211HFJI/), [IGVFFI4981QRBU](/sequence-files/IGVFFI4981QRBU/), [IGVFFI7831WEPE](/sequence-files/IGVFFI7831WEPE/), [IGVFFI9296JNYS](/sequence-files/IGVFFI9296JNYS/), [IGVFFI1277EBKM](/sequence-files/IGVFFI1277EBKM/), [IGVFFI2940UYKS](/sequence-files/IGVFFI2940UYKS/), [IGVFFI4062DZXY](/sequence-files/IGVFFI4062DZXY/), [IGVFFI6081UGVZ](/sequence-files/IGVFFI6081UGVZ/), [IGVFFI0134ACNG](/sequence-files/IGVFFI0134ACNG/), [IGVFFI9972QWZM](/sequence-files/IGVFFI9972QWZM/), [IGVFFI6937MHGN](/sequence-files/IGVFFI6937MHGN/), [IGVFFI1309XRYA](/sequence-files/IGVFFI1309XRYA/), [IGVFFI4261PVJC](/sequence-files/IGVFFI4261PVJC/), [IGVFFI7552MBTV](/sequence-files/IGVFFI7552MBTV/), [IGVFFI8012RRXD](/sequence-files/IGVFFI8012RRXD/), [IGVFFI6181NBYT](/sequence-files/IGVFFI6181NBYT/), [IGVFFI1064TWGN](/sequence-files/IGVFFI1064TWGN/), [IGVFFI0441JLWA](/sequence-files/IGVFFI0441JLWA/), [IGVFFI6813LUGK](/sequence-files/IGVFFI6813LUGK/), [IGVFFI7761WZTQ](/sequence-files/IGVFFI7761WZTQ/), [IGVFFI6849HRJB](/sequence-files/IGVFFI6849HRJB/) 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/IGVFDS8040RMZU/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8040RMZU](/auxiliary-sets/IGVFDS8040RMZU/) 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/IGVFDS8040RMZU/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8040RMZU/",
"accession": "IGVFDS8040RMZU",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:48.133719+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": "2023-12-20T23:08:02.514091+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6196LFWY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6196LFWY",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-BinB"
],
"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 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": "2023-12-13T09:15:41.201585+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": "bb8e5f27-797d-49cc-9c1b-63ddd4f1c4be"
}