{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0333TAKU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0333TAKU",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-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 [IGVFSM7887QAEK](/in-vitro-systems/IGVFSM7887QAEK/) 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/IGVFSM7887QAEK/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0333TAKU](/measurement-sets/IGVFDS0333TAKU/) has in progress subobject auxiliary set [IGVFDS0557FRZM](/auxiliary-sets/IGVFDS0557FRZM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0333TAKU/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0333TAKU](/measurement-sets/IGVFDS0333TAKU/) 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/IGVFDS0333TAKU/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0557FRZM](/auxiliary-sets/IGVFDS0557FRZM/) has sequence file(s) [IGVFFI6196BAOW](/sequence-files/IGVFFI6196BAOW/), [IGVFFI1845WBIW](/sequence-files/IGVFFI1845WBIW/), [IGVFFI5662SNOZ](/sequence-files/IGVFFI5662SNOZ/), [IGVFFI1431VMMF](/sequence-files/IGVFFI1431VMMF/), [IGVFFI4918WGKK](/sequence-files/IGVFFI4918WGKK/), [IGVFFI9036LSPR](/sequence-files/IGVFFI9036LSPR/), [IGVFFI4569XYJP](/sequence-files/IGVFFI4569XYJP/), [IGVFFI9831JAXI](/sequence-files/IGVFFI9831JAXI/), [IGVFFI3476MBUB](/sequence-files/IGVFFI3476MBUB/), [IGVFFI6945HKHO](/sequence-files/IGVFFI6945HKHO/), [IGVFFI3774EFGR](/sequence-files/IGVFFI3774EFGR/), [IGVFFI4920SLPO](/sequence-files/IGVFFI4920SLPO/), [IGVFFI3261KWLF](/sequence-files/IGVFFI3261KWLF/), [IGVFFI1462PDEY](/sequence-files/IGVFFI1462PDEY/), [IGVFFI8707LFXT](/sequence-files/IGVFFI8707LFXT/), [IGVFFI8793NYKD](/sequence-files/IGVFFI8793NYKD/), [IGVFFI5316SRFE](/sequence-files/IGVFFI5316SRFE/), [IGVFFI2848WEPJ](/sequence-files/IGVFFI2848WEPJ/), [IGVFFI5274TVBZ](/sequence-files/IGVFFI5274TVBZ/), [IGVFFI7099BDRG](/sequence-files/IGVFFI7099BDRG/), [IGVFFI4398XITN](/sequence-files/IGVFFI4398XITN/), [IGVFFI5731OQND](/sequence-files/IGVFFI5731OQND/), [IGVFFI4367KBDD](/sequence-files/IGVFFI4367KBDD/), [IGVFFI4575KAIW](/sequence-files/IGVFFI4575KAIW/), [IGVFFI2921IEOK](/sequence-files/IGVFFI2921IEOK/), [IGVFFI9654RPED](/sequence-files/IGVFFI9654RPED/), [IGVFFI0352WGND](/sequence-files/IGVFFI0352WGND/), [IGVFFI1064UYZV](/sequence-files/IGVFFI1064UYZV/), [IGVFFI8000AXTW](/sequence-files/IGVFFI8000AXTW/), [IGVFFI0222FTDC](/sequence-files/IGVFFI0222FTDC/), [IGVFFI5051HZOM](/sequence-files/IGVFFI5051HZOM/), [IGVFFI4920UPLF](/sequence-files/IGVFFI4920UPLF/), [IGVFFI8249RMDX](/sequence-files/IGVFFI8249RMDX/), [IGVFFI6720ZEEX](/sequence-files/IGVFFI6720ZEEX/), [IGVFFI8627SPVH](/sequence-files/IGVFFI8627SPVH/), [IGVFFI5007IUMS](/sequence-files/IGVFFI5007IUMS/), [IGVFFI6204GUIT](/sequence-files/IGVFFI6204GUIT/), [IGVFFI1426BWAB](/sequence-files/IGVFFI1426BWAB/), [IGVFFI2646YWCX](/sequence-files/IGVFFI2646YWCX/), [IGVFFI8822TWFI](/sequence-files/IGVFFI8822TWFI/), [IGVFFI5701UGPX](/sequence-files/IGVFFI5701UGPX/), [IGVFFI6991FPKD](/sequence-files/IGVFFI6991FPKD/), [IGVFFI1562GJLN](/sequence-files/IGVFFI1562GJLN/), [IGVFFI3707PDQM](/sequence-files/IGVFFI3707PDQM/), [IGVFFI8297FNWK](/sequence-files/IGVFFI8297FNWK/), [IGVFFI6766RHAF](/sequence-files/IGVFFI6766RHAF/), [IGVFFI0174USAR](/sequence-files/IGVFFI0174USAR/) 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/IGVFDS0557FRZM/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0557FRZM](/auxiliary-sets/IGVFDS0557FRZM/) has sequence file(s): [IGVFFI6196BAOW](/sequence-files/IGVFFI6196BAOW/), [IGVFFI1845WBIW](/sequence-files/IGVFFI1845WBIW/), [IGVFFI5662SNOZ](/sequence-files/IGVFFI5662SNOZ/), [IGVFFI1431VMMF](/sequence-files/IGVFFI1431VMMF/), [IGVFFI4918WGKK](/sequence-files/IGVFFI4918WGKK/), [IGVFFI9036LSPR](/sequence-files/IGVFFI9036LSPR/), [IGVFFI4569XYJP](/sequence-files/IGVFFI4569XYJP/), [IGVFFI9831JAXI](/sequence-files/IGVFFI9831JAXI/), [IGVFFI3476MBUB](/sequence-files/IGVFFI3476MBUB/), [IGVFFI6945HKHO](/sequence-files/IGVFFI6945HKHO/), [IGVFFI3774EFGR](/sequence-files/IGVFFI3774EFGR/), [IGVFFI4920SLPO](/sequence-files/IGVFFI4920SLPO/), [IGVFFI3261KWLF](/sequence-files/IGVFFI3261KWLF/), [IGVFFI1462PDEY](/sequence-files/IGVFFI1462PDEY/), [IGVFFI8707LFXT](/sequence-files/IGVFFI8707LFXT/), [IGVFFI8793NYKD](/sequence-files/IGVFFI8793NYKD/), [IGVFFI5316SRFE](/sequence-files/IGVFFI5316SRFE/), [IGVFFI2848WEPJ](/sequence-files/IGVFFI2848WEPJ/), [IGVFFI5274TVBZ](/sequence-files/IGVFFI5274TVBZ/), [IGVFFI7099BDRG](/sequence-files/IGVFFI7099BDRG/), [IGVFFI4398XITN](/sequence-files/IGVFFI4398XITN/), [IGVFFI5731OQND](/sequence-files/IGVFFI5731OQND/), [IGVFFI4367KBDD](/sequence-files/IGVFFI4367KBDD/), [IGVFFI4575KAIW](/sequence-files/IGVFFI4575KAIW/), [IGVFFI2921IEOK](/sequence-files/IGVFFI2921IEOK/), [IGVFFI9654RPED](/sequence-files/IGVFFI9654RPED/), [IGVFFI0352WGND](/sequence-files/IGVFFI0352WGND/), [IGVFFI1064UYZV](/sequence-files/IGVFFI1064UYZV/), [IGVFFI8000AXTW](/sequence-files/IGVFFI8000AXTW/), [IGVFFI0222FTDC](/sequence-files/IGVFFI0222FTDC/), [IGVFFI5051HZOM](/sequence-files/IGVFFI5051HZOM/), [IGVFFI4920UPLF](/sequence-files/IGVFFI4920UPLF/), [IGVFFI8249RMDX](/sequence-files/IGVFFI8249RMDX/), [IGVFFI6720ZEEX](/sequence-files/IGVFFI6720ZEEX/), [IGVFFI8627SPVH](/sequence-files/IGVFFI8627SPVH/), [IGVFFI5007IUMS](/sequence-files/IGVFFI5007IUMS/), [IGVFFI6204GUIT](/sequence-files/IGVFFI6204GUIT/), [IGVFFI1426BWAB](/sequence-files/IGVFFI1426BWAB/), [IGVFFI2646YWCX](/sequence-files/IGVFFI2646YWCX/), [IGVFFI8822TWFI](/sequence-files/IGVFFI8822TWFI/), [IGVFFI5701UGPX](/sequence-files/IGVFFI5701UGPX/), [IGVFFI6991FPKD](/sequence-files/IGVFFI6991FPKD/), [IGVFFI1562GJLN](/sequence-files/IGVFFI1562GJLN/), [IGVFFI3707PDQM](/sequence-files/IGVFFI3707PDQM/), [IGVFFI8297FNWK](/sequence-files/IGVFFI8297FNWK/), [IGVFFI6766RHAF](/sequence-files/IGVFFI6766RHAF/), [IGVFFI0174USAR](/sequence-files/IGVFFI0174USAR/) 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/IGVFDS0557FRZM/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0557FRZM](/auxiliary-sets/IGVFDS0557FRZM/) 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/IGVFDS0557FRZM/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0557FRZM/",
"accession": "IGVFDS0557FRZM",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-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": "2023-12-13T08:48:14.810527+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": "2023-12-20T23:09:00.719665+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7887QAEK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7887QAEK",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-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": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T10:24:16.058647+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": "f3a508a6-9a40-40e7-8808-1b68515c8341"
}