{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0974QLVO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0974QLVO",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep4-BinC_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 [IGVFDS0974QLVO](/measurement-sets/IGVFDS0974QLVO/) has in progress subobject auxiliary set [IGVFDS7873WZQT](/auxiliary-sets/IGVFDS7873WZQT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0974QLVO/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8798UNXX](/in-vitro-systems/IGVFSM8798UNXX/) 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/IGVFSM8798UNXX/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0974QLVO](/measurement-sets/IGVFDS0974QLVO/) 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/IGVFDS0974QLVO/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7873WZQT](/auxiliary-sets/IGVFDS7873WZQT/) has sequence file(s): [IGVFFI7952PGYG](/sequence-files/IGVFFI7952PGYG/), [IGVFFI9194FNVP](/sequence-files/IGVFFI9194FNVP/), [IGVFFI2106VZVV](/sequence-files/IGVFFI2106VZVV/), [IGVFFI9749IBXF](/sequence-files/IGVFFI9749IBXF/), [IGVFFI2930PAYZ](/sequence-files/IGVFFI2930PAYZ/), [IGVFFI9959VOXF](/sequence-files/IGVFFI9959VOXF/), [IGVFFI1810SCSG](/sequence-files/IGVFFI1810SCSG/), [IGVFFI3585MBYB](/sequence-files/IGVFFI3585MBYB/), [IGVFFI4435GQBC](/sequence-files/IGVFFI4435GQBC/), [IGVFFI1243NKNI](/sequence-files/IGVFFI1243NKNI/), [IGVFFI0124CFMN](/sequence-files/IGVFFI0124CFMN/), [IGVFFI2952CHMR](/sequence-files/IGVFFI2952CHMR/), [IGVFFI4569XAWR](/sequence-files/IGVFFI4569XAWR/), [IGVFFI3057ZJKD](/sequence-files/IGVFFI3057ZJKD/), [IGVFFI4142CADT](/sequence-files/IGVFFI4142CADT/), [IGVFFI9107KDEP](/sequence-files/IGVFFI9107KDEP/), [IGVFFI3023GTGL](/sequence-files/IGVFFI3023GTGL/), [IGVFFI4953AYXY](/sequence-files/IGVFFI4953AYXY/), [IGVFFI7522RYZS](/sequence-files/IGVFFI7522RYZS/), [IGVFFI9630INDK](/sequence-files/IGVFFI9630INDK/), [IGVFFI1710GPDZ](/sequence-files/IGVFFI1710GPDZ/), [IGVFFI5493LLRO](/sequence-files/IGVFFI5493LLRO/), [IGVFFI6157IKDE](/sequence-files/IGVFFI6157IKDE/), [IGVFFI5478DROE](/sequence-files/IGVFFI5478DROE/), [IGVFFI9649BAQU](/sequence-files/IGVFFI9649BAQU/), [IGVFFI7839PZWY](/sequence-files/IGVFFI7839PZWY/), [IGVFFI9686ZXPR](/sequence-files/IGVFFI9686ZXPR/), [IGVFFI3003OHQW](/sequence-files/IGVFFI3003OHQW/), [IGVFFI4646QREH](/sequence-files/IGVFFI4646QREH/), [IGVFFI9671REGY](/sequence-files/IGVFFI9671REGY/), [IGVFFI7465UGUQ](/sequence-files/IGVFFI7465UGUQ/), [IGVFFI6058QTDD](/sequence-files/IGVFFI6058QTDD/), [IGVFFI9824LCJE](/sequence-files/IGVFFI9824LCJE/), [IGVFFI0107ZPQB](/sequence-files/IGVFFI0107ZPQB/), [IGVFFI4269JBKC](/sequence-files/IGVFFI4269JBKC/), [IGVFFI4114PFHK](/sequence-files/IGVFFI4114PFHK/), [IGVFFI3037YHVZ](/sequence-files/IGVFFI3037YHVZ/), [IGVFFI2256WABA](/sequence-files/IGVFFI2256WABA/), [IGVFFI6851KBBB](/sequence-files/IGVFFI6851KBBB/), [IGVFFI5736XJTC](/sequence-files/IGVFFI5736XJTC/), [IGVFFI8425IBKP](/sequence-files/IGVFFI8425IBKP/), [IGVFFI4233RMDA](/sequence-files/IGVFFI4233RMDA/), [IGVFFI7215BWQB](/sequence-files/IGVFFI7215BWQB/), [IGVFFI6142AQUH](/sequence-files/IGVFFI6142AQUH/), [IGVFFI2733TORX](/sequence-files/IGVFFI2733TORX/), [IGVFFI8453XOAD](/sequence-files/IGVFFI8453XOAD/), [IGVFFI9549IOAW](/sequence-files/IGVFFI9549IOAW/), [IGVFFI6528MGLF](/sequence-files/IGVFFI6528MGLF/) 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/IGVFDS7873WZQT/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7873WZQT](/auxiliary-sets/IGVFDS7873WZQT/) has sequence file(s) [IGVFFI7952PGYG](/sequence-files/IGVFFI7952PGYG/), [IGVFFI9194FNVP](/sequence-files/IGVFFI9194FNVP/), [IGVFFI2106VZVV](/sequence-files/IGVFFI2106VZVV/), [IGVFFI9749IBXF](/sequence-files/IGVFFI9749IBXF/), [IGVFFI2930PAYZ](/sequence-files/IGVFFI2930PAYZ/), [IGVFFI9959VOXF](/sequence-files/IGVFFI9959VOXF/), [IGVFFI1810SCSG](/sequence-files/IGVFFI1810SCSG/), [IGVFFI3585MBYB](/sequence-files/IGVFFI3585MBYB/), [IGVFFI4435GQBC](/sequence-files/IGVFFI4435GQBC/), [IGVFFI1243NKNI](/sequence-files/IGVFFI1243NKNI/), [IGVFFI0124CFMN](/sequence-files/IGVFFI0124CFMN/), [IGVFFI2952CHMR](/sequence-files/IGVFFI2952CHMR/), [IGVFFI4569XAWR](/sequence-files/IGVFFI4569XAWR/), [IGVFFI3057ZJKD](/sequence-files/IGVFFI3057ZJKD/), [IGVFFI4142CADT](/sequence-files/IGVFFI4142CADT/), [IGVFFI9107KDEP](/sequence-files/IGVFFI9107KDEP/), [IGVFFI3023GTGL](/sequence-files/IGVFFI3023GTGL/), [IGVFFI4953AYXY](/sequence-files/IGVFFI4953AYXY/), [IGVFFI7522RYZS](/sequence-files/IGVFFI7522RYZS/), [IGVFFI9630INDK](/sequence-files/IGVFFI9630INDK/), [IGVFFI1710GPDZ](/sequence-files/IGVFFI1710GPDZ/), [IGVFFI5493LLRO](/sequence-files/IGVFFI5493LLRO/), [IGVFFI6157IKDE](/sequence-files/IGVFFI6157IKDE/), [IGVFFI5478DROE](/sequence-files/IGVFFI5478DROE/), [IGVFFI9649BAQU](/sequence-files/IGVFFI9649BAQU/), [IGVFFI7839PZWY](/sequence-files/IGVFFI7839PZWY/), [IGVFFI9686ZXPR](/sequence-files/IGVFFI9686ZXPR/), [IGVFFI3003OHQW](/sequence-files/IGVFFI3003OHQW/), [IGVFFI4646QREH](/sequence-files/IGVFFI4646QREH/), [IGVFFI9671REGY](/sequence-files/IGVFFI9671REGY/), [IGVFFI7465UGUQ](/sequence-files/IGVFFI7465UGUQ/), [IGVFFI6058QTDD](/sequence-files/IGVFFI6058QTDD/), [IGVFFI9824LCJE](/sequence-files/IGVFFI9824LCJE/), [IGVFFI0107ZPQB](/sequence-files/IGVFFI0107ZPQB/), [IGVFFI4269JBKC](/sequence-files/IGVFFI4269JBKC/), [IGVFFI4114PFHK](/sequence-files/IGVFFI4114PFHK/), [IGVFFI3037YHVZ](/sequence-files/IGVFFI3037YHVZ/), [IGVFFI2256WABA](/sequence-files/IGVFFI2256WABA/), [IGVFFI6851KBBB](/sequence-files/IGVFFI6851KBBB/), [IGVFFI5736XJTC](/sequence-files/IGVFFI5736XJTC/), [IGVFFI8425IBKP](/sequence-files/IGVFFI8425IBKP/), [IGVFFI4233RMDA](/sequence-files/IGVFFI4233RMDA/), [IGVFFI7215BWQB](/sequence-files/IGVFFI7215BWQB/), [IGVFFI6142AQUH](/sequence-files/IGVFFI6142AQUH/), [IGVFFI2733TORX](/sequence-files/IGVFFI2733TORX/), [IGVFFI8453XOAD](/sequence-files/IGVFFI8453XOAD/), [IGVFFI9549IOAW](/sequence-files/IGVFFI9549IOAW/), [IGVFFI6528MGLF](/sequence-files/IGVFFI6528MGLF/) 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/IGVFDS7873WZQT/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7873WZQT](/auxiliary-sets/IGVFDS7873WZQT/) 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/IGVFDS7873WZQT/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7873WZQT/",
"accession": "IGVFDS7873WZQT",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep4-BinC_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": "2023-12-13T08:48:08.717525+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": "2023-12-20T23:08:28.881747+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8798UNXX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8798UNXX",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep4-BinC"
],
"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 51-75% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "20",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T09:52:48.330991+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": "908e6d73-bd3d-4c70-a99f-4f3f98b47a7a"
}