{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5913QKWA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5913QKWA",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-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 measurement set [IGVFDS5913QKWA](/measurement-sets/IGVFDS5913QKWA/) has in progress subobject auxiliary set [IGVFDS8526DHDN](/auxiliary-sets/IGVFDS8526DHDN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5913QKWA/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7453CDOR](/in-vitro-systems/IGVFSM7453CDOR/) 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/IGVFSM7453CDOR/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5913QKWA](/measurement-sets/IGVFDS5913QKWA/) 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/IGVFDS5913QKWA/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8526DHDN](/auxiliary-sets/IGVFDS8526DHDN/) has sequence file(s): [IGVFFI5441YEJA](/sequence-files/IGVFFI5441YEJA/), [IGVFFI8165CTYL](/sequence-files/IGVFFI8165CTYL/), [IGVFFI3441EPFF](/sequence-files/IGVFFI3441EPFF/), [IGVFFI6748GXQW](/sequence-files/IGVFFI6748GXQW/), [IGVFFI8652HYNB](/sequence-files/IGVFFI8652HYNB/), [IGVFFI4689FPJI](/sequence-files/IGVFFI4689FPJI/), [IGVFFI5830XVIE](/sequence-files/IGVFFI5830XVIE/), [IGVFFI6090XTHK](/sequence-files/IGVFFI6090XTHK/), [IGVFFI5025AKHB](/sequence-files/IGVFFI5025AKHB/), [IGVFFI5833XPZA](/sequence-files/IGVFFI5833XPZA/), [IGVFFI2088RXNC](/sequence-files/IGVFFI2088RXNC/), [IGVFFI7614VLSQ](/sequence-files/IGVFFI7614VLSQ/), [IGVFFI2003BZPY](/sequence-files/IGVFFI2003BZPY/), [IGVFFI7951GGIK](/sequence-files/IGVFFI7951GGIK/), [IGVFFI5728XYGQ](/sequence-files/IGVFFI5728XYGQ/), [IGVFFI9261NDVX](/sequence-files/IGVFFI9261NDVX/), [IGVFFI5533FKIL](/sequence-files/IGVFFI5533FKIL/), [IGVFFI4664MANF](/sequence-files/IGVFFI4664MANF/), [IGVFFI2390FOKU](/sequence-files/IGVFFI2390FOKU/), [IGVFFI4190NQYP](/sequence-files/IGVFFI4190NQYP/), [IGVFFI0405HATV](/sequence-files/IGVFFI0405HATV/), [IGVFFI8452SDOL](/sequence-files/IGVFFI8452SDOL/), [IGVFFI8450ZXUO](/sequence-files/IGVFFI8450ZXUO/), [IGVFFI0503TXAP](/sequence-files/IGVFFI0503TXAP/), [IGVFFI0621COCJ](/sequence-files/IGVFFI0621COCJ/), [IGVFFI5566BYRL](/sequence-files/IGVFFI5566BYRL/), [IGVFFI2642HHPE](/sequence-files/IGVFFI2642HHPE/), [IGVFFI9018SBSM](/sequence-files/IGVFFI9018SBSM/), [IGVFFI7538WLJI](/sequence-files/IGVFFI7538WLJI/), [IGVFFI3149GIXS](/sequence-files/IGVFFI3149GIXS/), [IGVFFI2060GXOJ](/sequence-files/IGVFFI2060GXOJ/), [IGVFFI5629WMGP](/sequence-files/IGVFFI5629WMGP/), [IGVFFI2982BLYB](/sequence-files/IGVFFI2982BLYB/), [IGVFFI0234KSKE](/sequence-files/IGVFFI0234KSKE/), [IGVFFI1885WBEH](/sequence-files/IGVFFI1885WBEH/), [IGVFFI6606PLCG](/sequence-files/IGVFFI6606PLCG/), [IGVFFI7184BYWH](/sequence-files/IGVFFI7184BYWH/), [IGVFFI8977YYWC](/sequence-files/IGVFFI8977YYWC/), [IGVFFI9788RCRL](/sequence-files/IGVFFI9788RCRL/), [IGVFFI2069BDCH](/sequence-files/IGVFFI2069BDCH/), [IGVFFI3376QDOE](/sequence-files/IGVFFI3376QDOE/), [IGVFFI4854CJNH](/sequence-files/IGVFFI4854CJNH/), [IGVFFI7416QOPH](/sequence-files/IGVFFI7416QOPH/), [IGVFFI9264QXPY](/sequence-files/IGVFFI9264QXPY/), [IGVFFI7490FCDL](/sequence-files/IGVFFI7490FCDL/), [IGVFFI5538EBRB](/sequence-files/IGVFFI5538EBRB/), [IGVFFI2605SVTI](/sequence-files/IGVFFI2605SVTI/), [IGVFFI4880YDGX](/sequence-files/IGVFFI4880YDGX/) 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/IGVFDS8526DHDN/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8526DHDN](/auxiliary-sets/IGVFDS8526DHDN/) has sequence file(s) [IGVFFI5441YEJA](/sequence-files/IGVFFI5441YEJA/), [IGVFFI8165CTYL](/sequence-files/IGVFFI8165CTYL/), [IGVFFI3441EPFF](/sequence-files/IGVFFI3441EPFF/), [IGVFFI6748GXQW](/sequence-files/IGVFFI6748GXQW/), [IGVFFI8652HYNB](/sequence-files/IGVFFI8652HYNB/), [IGVFFI4689FPJI](/sequence-files/IGVFFI4689FPJI/), [IGVFFI5830XVIE](/sequence-files/IGVFFI5830XVIE/), [IGVFFI6090XTHK](/sequence-files/IGVFFI6090XTHK/), [IGVFFI5025AKHB](/sequence-files/IGVFFI5025AKHB/), [IGVFFI5833XPZA](/sequence-files/IGVFFI5833XPZA/), [IGVFFI2088RXNC](/sequence-files/IGVFFI2088RXNC/), [IGVFFI7614VLSQ](/sequence-files/IGVFFI7614VLSQ/), [IGVFFI2003BZPY](/sequence-files/IGVFFI2003BZPY/), [IGVFFI7951GGIK](/sequence-files/IGVFFI7951GGIK/), [IGVFFI5728XYGQ](/sequence-files/IGVFFI5728XYGQ/), [IGVFFI9261NDVX](/sequence-files/IGVFFI9261NDVX/), [IGVFFI5533FKIL](/sequence-files/IGVFFI5533FKIL/), [IGVFFI4664MANF](/sequence-files/IGVFFI4664MANF/), [IGVFFI2390FOKU](/sequence-files/IGVFFI2390FOKU/), [IGVFFI4190NQYP](/sequence-files/IGVFFI4190NQYP/), [IGVFFI0405HATV](/sequence-files/IGVFFI0405HATV/), [IGVFFI8452SDOL](/sequence-files/IGVFFI8452SDOL/), [IGVFFI8450ZXUO](/sequence-files/IGVFFI8450ZXUO/), [IGVFFI0503TXAP](/sequence-files/IGVFFI0503TXAP/), [IGVFFI0621COCJ](/sequence-files/IGVFFI0621COCJ/), [IGVFFI5566BYRL](/sequence-files/IGVFFI5566BYRL/), [IGVFFI2642HHPE](/sequence-files/IGVFFI2642HHPE/), [IGVFFI9018SBSM](/sequence-files/IGVFFI9018SBSM/), [IGVFFI7538WLJI](/sequence-files/IGVFFI7538WLJI/), [IGVFFI3149GIXS](/sequence-files/IGVFFI3149GIXS/), [IGVFFI2060GXOJ](/sequence-files/IGVFFI2060GXOJ/), [IGVFFI5629WMGP](/sequence-files/IGVFFI5629WMGP/), [IGVFFI2982BLYB](/sequence-files/IGVFFI2982BLYB/), [IGVFFI0234KSKE](/sequence-files/IGVFFI0234KSKE/), [IGVFFI1885WBEH](/sequence-files/IGVFFI1885WBEH/), [IGVFFI6606PLCG](/sequence-files/IGVFFI6606PLCG/), [IGVFFI7184BYWH](/sequence-files/IGVFFI7184BYWH/), [IGVFFI8977YYWC](/sequence-files/IGVFFI8977YYWC/), [IGVFFI9788RCRL](/sequence-files/IGVFFI9788RCRL/), [IGVFFI2069BDCH](/sequence-files/IGVFFI2069BDCH/), [IGVFFI3376QDOE](/sequence-files/IGVFFI3376QDOE/), [IGVFFI4854CJNH](/sequence-files/IGVFFI4854CJNH/), [IGVFFI7416QOPH](/sequence-files/IGVFFI7416QOPH/), [IGVFFI9264QXPY](/sequence-files/IGVFFI9264QXPY/), [IGVFFI7490FCDL](/sequence-files/IGVFFI7490FCDL/), [IGVFFI5538EBRB](/sequence-files/IGVFFI5538EBRB/), [IGVFFI2605SVTI](/sequence-files/IGVFFI2605SVTI/), [IGVFFI4880YDGX](/sequence-files/IGVFFI4880YDGX/) 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/IGVFDS8526DHDN/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8526DHDN](/auxiliary-sets/IGVFDS8526DHDN/) 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/IGVFDS8526DHDN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8526DHDN/",
"accession": "IGVFDS8526DHDN",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:48:06.344965+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS6299IJHG/"
],
"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": "2023-12-20T23:08:50.443160+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7453CDOR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7453CDOR",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-BinA"
],
"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_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat 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": "2023-12-13T09:44:21.813738+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": "d49b8a0c-bcfe-44d9-a53c-786dd3bf2448"
}