{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4852VNMA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4852VNMA",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep2-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 [IGVFDS4852VNMA](/measurement-sets/IGVFDS4852VNMA/) has in progress subobject auxiliary set [IGVFDS5518GLYA](/auxiliary-sets/IGVFDS5518GLYA/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4852VNMA/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5940SWOY](/in-vitro-systems/IGVFSM5940SWOY/) 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/IGVFSM5940SWOY/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5518GLYA](/auxiliary-sets/IGVFDS5518GLYA/) has sequence file(s): [IGVFFI9583LCAE](/sequence-files/IGVFFI9583LCAE/), [IGVFFI5185UQCS](/sequence-files/IGVFFI5185UQCS/), [IGVFFI3707TNKP](/sequence-files/IGVFFI3707TNKP/), [IGVFFI8955ESDA](/sequence-files/IGVFFI8955ESDA/), [IGVFFI6091YVJO](/sequence-files/IGVFFI6091YVJO/), [IGVFFI2097ZFJO](/sequence-files/IGVFFI2097ZFJO/), [IGVFFI7629FYOP](/sequence-files/IGVFFI7629FYOP/), [IGVFFI3302BNTV](/sequence-files/IGVFFI3302BNTV/), [IGVFFI5647AVPS](/sequence-files/IGVFFI5647AVPS/), [IGVFFI1698UCNY](/sequence-files/IGVFFI1698UCNY/), [IGVFFI6163RBZZ](/sequence-files/IGVFFI6163RBZZ/), [IGVFFI2055YBKY](/sequence-files/IGVFFI2055YBKY/), [IGVFFI6824LCAA](/sequence-files/IGVFFI6824LCAA/), [IGVFFI3392TSTR](/sequence-files/IGVFFI3392TSTR/), [IGVFFI2505TXTG](/sequence-files/IGVFFI2505TXTG/), [IGVFFI6419AKER](/sequence-files/IGVFFI6419AKER/), [IGVFFI0727FXUL](/sequence-files/IGVFFI0727FXUL/), [IGVFFI9069WYAM](/sequence-files/IGVFFI9069WYAM/), [IGVFFI7740RHKM](/sequence-files/IGVFFI7740RHKM/), [IGVFFI8497PPDU](/sequence-files/IGVFFI8497PPDU/), [IGVFFI7004EZNE](/sequence-files/IGVFFI7004EZNE/), [IGVFFI3151VCTM](/sequence-files/IGVFFI3151VCTM/), [IGVFFI4081NYFS](/sequence-files/IGVFFI4081NYFS/), [IGVFFI2889XXGS](/sequence-files/IGVFFI2889XXGS/), [IGVFFI7795KGDQ](/sequence-files/IGVFFI7795KGDQ/), [IGVFFI9149EIBE](/sequence-files/IGVFFI9149EIBE/), [IGVFFI0467LSPA](/sequence-files/IGVFFI0467LSPA/), [IGVFFI6643OFJW](/sequence-files/IGVFFI6643OFJW/), [IGVFFI9924HYJT](/sequence-files/IGVFFI9924HYJT/), [IGVFFI5742MUGU](/sequence-files/IGVFFI5742MUGU/), [IGVFFI3027UAID](/sequence-files/IGVFFI3027UAID/), [IGVFFI0827UVKC](/sequence-files/IGVFFI0827UVKC/), [IGVFFI8355SQSX](/sequence-files/IGVFFI8355SQSX/), [IGVFFI4548ADIC](/sequence-files/IGVFFI4548ADIC/), [IGVFFI3275BTUR](/sequence-files/IGVFFI3275BTUR/), [IGVFFI8482JNFU](/sequence-files/IGVFFI8482JNFU/), [IGVFFI5381OAFZ](/sequence-files/IGVFFI5381OAFZ/), [IGVFFI7920NTXB](/sequence-files/IGVFFI7920NTXB/), [IGVFFI2572XQJC](/sequence-files/IGVFFI2572XQJC/), [IGVFFI9404JQYW](/sequence-files/IGVFFI9404JQYW/), [IGVFFI5188GNCD](/sequence-files/IGVFFI5188GNCD/), [IGVFFI4819PAZA](/sequence-files/IGVFFI4819PAZA/), [IGVFFI2368KUJL](/sequence-files/IGVFFI2368KUJL/), [IGVFFI9695NQYQ](/sequence-files/IGVFFI9695NQYQ/), [IGVFFI5709MHPH](/sequence-files/IGVFFI5709MHPH/), [IGVFFI7397EKNW](/sequence-files/IGVFFI7397EKNW/), [IGVFFI3214MEFX](/sequence-files/IGVFFI3214MEFX/), [IGVFFI8021VYQB](/sequence-files/IGVFFI8021VYQB/) 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/IGVFDS5518GLYA/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4852VNMA](/measurement-sets/IGVFDS4852VNMA/) 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/IGVFDS4852VNMA/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5518GLYA](/auxiliary-sets/IGVFDS5518GLYA/) has sequence file(s) [IGVFFI9583LCAE](/sequence-files/IGVFFI9583LCAE/), [IGVFFI5185UQCS](/sequence-files/IGVFFI5185UQCS/), [IGVFFI3707TNKP](/sequence-files/IGVFFI3707TNKP/), [IGVFFI8955ESDA](/sequence-files/IGVFFI8955ESDA/), [IGVFFI6091YVJO](/sequence-files/IGVFFI6091YVJO/), [IGVFFI2097ZFJO](/sequence-files/IGVFFI2097ZFJO/), [IGVFFI7629FYOP](/sequence-files/IGVFFI7629FYOP/), [IGVFFI3302BNTV](/sequence-files/IGVFFI3302BNTV/), [IGVFFI5647AVPS](/sequence-files/IGVFFI5647AVPS/), [IGVFFI1698UCNY](/sequence-files/IGVFFI1698UCNY/), [IGVFFI6163RBZZ](/sequence-files/IGVFFI6163RBZZ/), [IGVFFI2055YBKY](/sequence-files/IGVFFI2055YBKY/), [IGVFFI6824LCAA](/sequence-files/IGVFFI6824LCAA/), [IGVFFI3392TSTR](/sequence-files/IGVFFI3392TSTR/), [IGVFFI2505TXTG](/sequence-files/IGVFFI2505TXTG/), [IGVFFI6419AKER](/sequence-files/IGVFFI6419AKER/), [IGVFFI0727FXUL](/sequence-files/IGVFFI0727FXUL/), [IGVFFI9069WYAM](/sequence-files/IGVFFI9069WYAM/), [IGVFFI7740RHKM](/sequence-files/IGVFFI7740RHKM/), [IGVFFI8497PPDU](/sequence-files/IGVFFI8497PPDU/), [IGVFFI7004EZNE](/sequence-files/IGVFFI7004EZNE/), [IGVFFI3151VCTM](/sequence-files/IGVFFI3151VCTM/), [IGVFFI4081NYFS](/sequence-files/IGVFFI4081NYFS/), [IGVFFI2889XXGS](/sequence-files/IGVFFI2889XXGS/), [IGVFFI7795KGDQ](/sequence-files/IGVFFI7795KGDQ/), [IGVFFI9149EIBE](/sequence-files/IGVFFI9149EIBE/), [IGVFFI0467LSPA](/sequence-files/IGVFFI0467LSPA/), [IGVFFI6643OFJW](/sequence-files/IGVFFI6643OFJW/), [IGVFFI9924HYJT](/sequence-files/IGVFFI9924HYJT/), [IGVFFI5742MUGU](/sequence-files/IGVFFI5742MUGU/), [IGVFFI3027UAID](/sequence-files/IGVFFI3027UAID/), [IGVFFI0827UVKC](/sequence-files/IGVFFI0827UVKC/), [IGVFFI8355SQSX](/sequence-files/IGVFFI8355SQSX/), [IGVFFI4548ADIC](/sequence-files/IGVFFI4548ADIC/), [IGVFFI3275BTUR](/sequence-files/IGVFFI3275BTUR/), [IGVFFI8482JNFU](/sequence-files/IGVFFI8482JNFU/), [IGVFFI5381OAFZ](/sequence-files/IGVFFI5381OAFZ/), [IGVFFI7920NTXB](/sequence-files/IGVFFI7920NTXB/), [IGVFFI2572XQJC](/sequence-files/IGVFFI2572XQJC/), [IGVFFI9404JQYW](/sequence-files/IGVFFI9404JQYW/), [IGVFFI5188GNCD](/sequence-files/IGVFFI5188GNCD/), [IGVFFI4819PAZA](/sequence-files/IGVFFI4819PAZA/), [IGVFFI2368KUJL](/sequence-files/IGVFFI2368KUJL/), [IGVFFI9695NQYQ](/sequence-files/IGVFFI9695NQYQ/), [IGVFFI5709MHPH](/sequence-files/IGVFFI5709MHPH/), [IGVFFI7397EKNW](/sequence-files/IGVFFI7397EKNW/), [IGVFFI3214MEFX](/sequence-files/IGVFFI3214MEFX/), [IGVFFI8021VYQB](/sequence-files/IGVFFI8021VYQB/) 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/IGVFDS5518GLYA/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5518GLYA](/auxiliary-sets/IGVFDS5518GLYA/) 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/IGVFDS5518GLYA/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5518GLYA/",
"accession": "IGVFDS5518GLYA",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep2-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": "2023-12-13T08:48:12.144043+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": "2023-12-20T23:08:20.314191+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5940SWOY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5940SWOY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep2-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": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T10:08:40.833198+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": "264d7d29-2831-46f5-89b0-b7a720d7c232"
}