{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4884AZCV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4884AZCV",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-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 in vitro system [IGVFSM2669ZPPW](/in-vitro-systems/IGVFSM2669ZPPW/) 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/IGVFSM2669ZPPW/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4884AZCV](/measurement-sets/IGVFDS4884AZCV/) has in progress subobject auxiliary set [IGVFDS7500MTYV](/auxiliary-sets/IGVFDS7500MTYV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4884AZCV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4884AZCV](/measurement-sets/IGVFDS4884AZCV/) 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/IGVFDS4884AZCV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7500MTYV](/auxiliary-sets/IGVFDS7500MTYV/) has sequence file(s): [IGVFFI1628MTGM](/sequence-files/IGVFFI1628MTGM/), [IGVFFI1954QKSK](/sequence-files/IGVFFI1954QKSK/), [IGVFFI7652YEES](/sequence-files/IGVFFI7652YEES/), [IGVFFI4082YCIT](/sequence-files/IGVFFI4082YCIT/), [IGVFFI4804TGEI](/sequence-files/IGVFFI4804TGEI/), [IGVFFI5353PQMM](/sequence-files/IGVFFI5353PQMM/), [IGVFFI5866PVRR](/sequence-files/IGVFFI5866PVRR/), [IGVFFI1300VJTD](/sequence-files/IGVFFI1300VJTD/), [IGVFFI2122AXMH](/sequence-files/IGVFFI2122AXMH/), [IGVFFI8446ZPIL](/sequence-files/IGVFFI8446ZPIL/), [IGVFFI0979OTQU](/sequence-files/IGVFFI0979OTQU/), [IGVFFI9980MEDM](/sequence-files/IGVFFI9980MEDM/), [IGVFFI6886YTHD](/sequence-files/IGVFFI6886YTHD/), [IGVFFI9971ADMC](/sequence-files/IGVFFI9971ADMC/), [IGVFFI1588RUBD](/sequence-files/IGVFFI1588RUBD/), [IGVFFI8423WIQE](/sequence-files/IGVFFI8423WIQE/), [IGVFFI3661UNHI](/sequence-files/IGVFFI3661UNHI/), [IGVFFI3855AKDI](/sequence-files/IGVFFI3855AKDI/), [IGVFFI4463UIDR](/sequence-files/IGVFFI4463UIDR/), [IGVFFI1678BEDQ](/sequence-files/IGVFFI1678BEDQ/), [IGVFFI0849NWWT](/sequence-files/IGVFFI0849NWWT/), [IGVFFI8588UEYA](/sequence-files/IGVFFI8588UEYA/), [IGVFFI2009GYBY](/sequence-files/IGVFFI2009GYBY/), [IGVFFI1520HRTG](/sequence-files/IGVFFI1520HRTG/), [IGVFFI8818NJYF](/sequence-files/IGVFFI8818NJYF/), [IGVFFI3591SJHJ](/sequence-files/IGVFFI3591SJHJ/), [IGVFFI8525WUVG](/sequence-files/IGVFFI8525WUVG/), [IGVFFI1271LZAA](/sequence-files/IGVFFI1271LZAA/), [IGVFFI1628AYDK](/sequence-files/IGVFFI1628AYDK/), [IGVFFI8305YDEX](/sequence-files/IGVFFI8305YDEX/), [IGVFFI0815YBPI](/sequence-files/IGVFFI0815YBPI/), [IGVFFI7070AVRZ](/sequence-files/IGVFFI7070AVRZ/), [IGVFFI5620NJWM](/sequence-files/IGVFFI5620NJWM/), [IGVFFI2005SFWU](/sequence-files/IGVFFI2005SFWU/), [IGVFFI2793ZTOK](/sequence-files/IGVFFI2793ZTOK/), [IGVFFI4694PVJE](/sequence-files/IGVFFI4694PVJE/), [IGVFFI1551NSZC](/sequence-files/IGVFFI1551NSZC/), [IGVFFI9393SDZG](/sequence-files/IGVFFI9393SDZG/), [IGVFFI5240BITR](/sequence-files/IGVFFI5240BITR/), [IGVFFI5861LUNW](/sequence-files/IGVFFI5861LUNW/), [IGVFFI8328AQFO](/sequence-files/IGVFFI8328AQFO/), [IGVFFI6970NWCX](/sequence-files/IGVFFI6970NWCX/), [IGVFFI5406WEQG](/sequence-files/IGVFFI5406WEQG/), [IGVFFI7937MOKO](/sequence-files/IGVFFI7937MOKO/), [IGVFFI6636CRXI](/sequence-files/IGVFFI6636CRXI/), [IGVFFI5649RFFQ](/sequence-files/IGVFFI5649RFFQ/), [IGVFFI0312MGAT](/sequence-files/IGVFFI0312MGAT/), [IGVFFI8190QXAC](/sequence-files/IGVFFI8190QXAC/) 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/IGVFDS7500MTYV/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7500MTYV](/auxiliary-sets/IGVFDS7500MTYV/) has sequence file(s) [IGVFFI1628MTGM](/sequence-files/IGVFFI1628MTGM/), [IGVFFI1954QKSK](/sequence-files/IGVFFI1954QKSK/), [IGVFFI7652YEES](/sequence-files/IGVFFI7652YEES/), [IGVFFI4082YCIT](/sequence-files/IGVFFI4082YCIT/), [IGVFFI4804TGEI](/sequence-files/IGVFFI4804TGEI/), [IGVFFI5353PQMM](/sequence-files/IGVFFI5353PQMM/), [IGVFFI5866PVRR](/sequence-files/IGVFFI5866PVRR/), [IGVFFI1300VJTD](/sequence-files/IGVFFI1300VJTD/), [IGVFFI2122AXMH](/sequence-files/IGVFFI2122AXMH/), [IGVFFI8446ZPIL](/sequence-files/IGVFFI8446ZPIL/), [IGVFFI0979OTQU](/sequence-files/IGVFFI0979OTQU/), [IGVFFI9980MEDM](/sequence-files/IGVFFI9980MEDM/), [IGVFFI6886YTHD](/sequence-files/IGVFFI6886YTHD/), [IGVFFI9971ADMC](/sequence-files/IGVFFI9971ADMC/), [IGVFFI1588RUBD](/sequence-files/IGVFFI1588RUBD/), [IGVFFI8423WIQE](/sequence-files/IGVFFI8423WIQE/), [IGVFFI3661UNHI](/sequence-files/IGVFFI3661UNHI/), [IGVFFI3855AKDI](/sequence-files/IGVFFI3855AKDI/), [IGVFFI4463UIDR](/sequence-files/IGVFFI4463UIDR/), [IGVFFI1678BEDQ](/sequence-files/IGVFFI1678BEDQ/), [IGVFFI0849NWWT](/sequence-files/IGVFFI0849NWWT/), [IGVFFI8588UEYA](/sequence-files/IGVFFI8588UEYA/), [IGVFFI2009GYBY](/sequence-files/IGVFFI2009GYBY/), [IGVFFI1520HRTG](/sequence-files/IGVFFI1520HRTG/), [IGVFFI8818NJYF](/sequence-files/IGVFFI8818NJYF/), [IGVFFI3591SJHJ](/sequence-files/IGVFFI3591SJHJ/), [IGVFFI8525WUVG](/sequence-files/IGVFFI8525WUVG/), [IGVFFI1271LZAA](/sequence-files/IGVFFI1271LZAA/), [IGVFFI1628AYDK](/sequence-files/IGVFFI1628AYDK/), [IGVFFI8305YDEX](/sequence-files/IGVFFI8305YDEX/), [IGVFFI0815YBPI](/sequence-files/IGVFFI0815YBPI/), [IGVFFI7070AVRZ](/sequence-files/IGVFFI7070AVRZ/), [IGVFFI5620NJWM](/sequence-files/IGVFFI5620NJWM/), [IGVFFI2005SFWU](/sequence-files/IGVFFI2005SFWU/), [IGVFFI2793ZTOK](/sequence-files/IGVFFI2793ZTOK/), [IGVFFI4694PVJE](/sequence-files/IGVFFI4694PVJE/), [IGVFFI1551NSZC](/sequence-files/IGVFFI1551NSZC/), [IGVFFI9393SDZG](/sequence-files/IGVFFI9393SDZG/), [IGVFFI5240BITR](/sequence-files/IGVFFI5240BITR/), [IGVFFI5861LUNW](/sequence-files/IGVFFI5861LUNW/), [IGVFFI8328AQFO](/sequence-files/IGVFFI8328AQFO/), [IGVFFI6970NWCX](/sequence-files/IGVFFI6970NWCX/), [IGVFFI5406WEQG](/sequence-files/IGVFFI5406WEQG/), [IGVFFI7937MOKO](/sequence-files/IGVFFI7937MOKO/), [IGVFFI6636CRXI](/sequence-files/IGVFFI6636CRXI/), [IGVFFI5649RFFQ](/sequence-files/IGVFFI5649RFFQ/), [IGVFFI0312MGAT](/sequence-files/IGVFFI0312MGAT/), [IGVFFI8190QXAC](/sequence-files/IGVFFI8190QXAC/) 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/IGVFDS7500MTYV/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7500MTYV](/auxiliary-sets/IGVFDS7500MTYV/) 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/IGVFDS7500MTYV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7500MTYV/",
"accession": "IGVFDS7500MTYV",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-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": "2023-12-13T08:48:07.001825+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": "2023-12-20T23:08:17.247296+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2669ZPPW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2669ZPPW",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-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": "2023-12-13T09:44:44.405451+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": "d8342139-e51e-453a-a35e-ba8efbe1c107"
}