{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4752FLON/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4752FLON",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-BinB_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 [IGVFDS4752FLON](/measurement-sets/IGVFDS4752FLON/) has in progress subobject auxiliary set [IGVFDS1470QEOX](/auxiliary-sets/IGVFDS1470QEOX/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4752FLON/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1838USXI](/in-vitro-systems/IGVFSM1838USXI/) 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/IGVFSM1838USXI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4752FLON](/measurement-sets/IGVFDS4752FLON/) 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/IGVFDS4752FLON/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1470QEOX](/auxiliary-sets/IGVFDS1470QEOX/) has sequence file(s): [IGVFFI5454XMWM](/sequence-files/IGVFFI5454XMWM/), [IGVFFI5253KQNA](/sequence-files/IGVFFI5253KQNA/), [IGVFFI2816IJOL](/sequence-files/IGVFFI2816IJOL/), [IGVFFI4171NTKF](/sequence-files/IGVFFI4171NTKF/), [IGVFFI9218RWCU](/sequence-files/IGVFFI9218RWCU/), [IGVFFI1665PBUX](/sequence-files/IGVFFI1665PBUX/), [IGVFFI2673ZSJO](/sequence-files/IGVFFI2673ZSJO/), [IGVFFI6451VQAS](/sequence-files/IGVFFI6451VQAS/), [IGVFFI8562BHLG](/sequence-files/IGVFFI8562BHLG/), [IGVFFI8418DFET](/sequence-files/IGVFFI8418DFET/), [IGVFFI1749VWLS](/sequence-files/IGVFFI1749VWLS/), [IGVFFI4620UWTA](/sequence-files/IGVFFI4620UWTA/), [IGVFFI6356SBUM](/sequence-files/IGVFFI6356SBUM/), [IGVFFI2889NFNT](/sequence-files/IGVFFI2889NFNT/), [IGVFFI2309FCAH](/sequence-files/IGVFFI2309FCAH/), [IGVFFI2455DONN](/sequence-files/IGVFFI2455DONN/), [IGVFFI2966KTVV](/sequence-files/IGVFFI2966KTVV/), [IGVFFI7546AOIT](/sequence-files/IGVFFI7546AOIT/), [IGVFFI0944CZSS](/sequence-files/IGVFFI0944CZSS/), [IGVFFI8233CCAJ](/sequence-files/IGVFFI8233CCAJ/), [IGVFFI4315UCLC](/sequence-files/IGVFFI4315UCLC/), [IGVFFI4406DBQR](/sequence-files/IGVFFI4406DBQR/), [IGVFFI5911XZRL](/sequence-files/IGVFFI5911XZRL/), [IGVFFI9735OCYM](/sequence-files/IGVFFI9735OCYM/), [IGVFFI8015VDZA](/sequence-files/IGVFFI8015VDZA/), [IGVFFI6681LQPA](/sequence-files/IGVFFI6681LQPA/), [IGVFFI3061PCTG](/sequence-files/IGVFFI3061PCTG/), [IGVFFI0601WFWF](/sequence-files/IGVFFI0601WFWF/), [IGVFFI3807DWRT](/sequence-files/IGVFFI3807DWRT/), [IGVFFI1934NWYG](/sequence-files/IGVFFI1934NWYG/), [IGVFFI7666HMMV](/sequence-files/IGVFFI7666HMMV/), [IGVFFI9512QSXF](/sequence-files/IGVFFI9512QSXF/), [IGVFFI5457UYFE](/sequence-files/IGVFFI5457UYFE/), [IGVFFI5663OEVS](/sequence-files/IGVFFI5663OEVS/), [IGVFFI9058GJCO](/sequence-files/IGVFFI9058GJCO/), [IGVFFI4106OCGW](/sequence-files/IGVFFI4106OCGW/), [IGVFFI3401FTPY](/sequence-files/IGVFFI3401FTPY/), [IGVFFI3560JRAD](/sequence-files/IGVFFI3560JRAD/), [IGVFFI9608CCLH](/sequence-files/IGVFFI9608CCLH/), [IGVFFI2013KLCS](/sequence-files/IGVFFI2013KLCS/), [IGVFFI3590RFFA](/sequence-files/IGVFFI3590RFFA/), [IGVFFI4064LQPH](/sequence-files/IGVFFI4064LQPH/), [IGVFFI8614YIIT](/sequence-files/IGVFFI8614YIIT/), [IGVFFI4224TVST](/sequence-files/IGVFFI4224TVST/), [IGVFFI4196IBSF](/sequence-files/IGVFFI4196IBSF/), [IGVFFI2720CWNA](/sequence-files/IGVFFI2720CWNA/), [IGVFFI6885RUCL](/sequence-files/IGVFFI6885RUCL/), [IGVFFI2362JMED](/sequence-files/IGVFFI2362JMED/) 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/IGVFDS1470QEOX/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1470QEOX](/auxiliary-sets/IGVFDS1470QEOX/) has sequence file(s) [IGVFFI5454XMWM](/sequence-files/IGVFFI5454XMWM/), [IGVFFI5253KQNA](/sequence-files/IGVFFI5253KQNA/), [IGVFFI2816IJOL](/sequence-files/IGVFFI2816IJOL/), [IGVFFI4171NTKF](/sequence-files/IGVFFI4171NTKF/), [IGVFFI9218RWCU](/sequence-files/IGVFFI9218RWCU/), [IGVFFI1665PBUX](/sequence-files/IGVFFI1665PBUX/), [IGVFFI2673ZSJO](/sequence-files/IGVFFI2673ZSJO/), [IGVFFI6451VQAS](/sequence-files/IGVFFI6451VQAS/), [IGVFFI8562BHLG](/sequence-files/IGVFFI8562BHLG/), [IGVFFI8418DFET](/sequence-files/IGVFFI8418DFET/), [IGVFFI1749VWLS](/sequence-files/IGVFFI1749VWLS/), [IGVFFI4620UWTA](/sequence-files/IGVFFI4620UWTA/), [IGVFFI6356SBUM](/sequence-files/IGVFFI6356SBUM/), [IGVFFI2889NFNT](/sequence-files/IGVFFI2889NFNT/), [IGVFFI2309FCAH](/sequence-files/IGVFFI2309FCAH/), [IGVFFI2455DONN](/sequence-files/IGVFFI2455DONN/), [IGVFFI2966KTVV](/sequence-files/IGVFFI2966KTVV/), [IGVFFI7546AOIT](/sequence-files/IGVFFI7546AOIT/), [IGVFFI0944CZSS](/sequence-files/IGVFFI0944CZSS/), [IGVFFI8233CCAJ](/sequence-files/IGVFFI8233CCAJ/), [IGVFFI4315UCLC](/sequence-files/IGVFFI4315UCLC/), [IGVFFI4406DBQR](/sequence-files/IGVFFI4406DBQR/), [IGVFFI5911XZRL](/sequence-files/IGVFFI5911XZRL/), [IGVFFI9735OCYM](/sequence-files/IGVFFI9735OCYM/), [IGVFFI8015VDZA](/sequence-files/IGVFFI8015VDZA/), [IGVFFI6681LQPA](/sequence-files/IGVFFI6681LQPA/), [IGVFFI3061PCTG](/sequence-files/IGVFFI3061PCTG/), [IGVFFI0601WFWF](/sequence-files/IGVFFI0601WFWF/), [IGVFFI3807DWRT](/sequence-files/IGVFFI3807DWRT/), [IGVFFI1934NWYG](/sequence-files/IGVFFI1934NWYG/), [IGVFFI7666HMMV](/sequence-files/IGVFFI7666HMMV/), [IGVFFI9512QSXF](/sequence-files/IGVFFI9512QSXF/), [IGVFFI5457UYFE](/sequence-files/IGVFFI5457UYFE/), [IGVFFI5663OEVS](/sequence-files/IGVFFI5663OEVS/), [IGVFFI9058GJCO](/sequence-files/IGVFFI9058GJCO/), [IGVFFI4106OCGW](/sequence-files/IGVFFI4106OCGW/), [IGVFFI3401FTPY](/sequence-files/IGVFFI3401FTPY/), [IGVFFI3560JRAD](/sequence-files/IGVFFI3560JRAD/), [IGVFFI9608CCLH](/sequence-files/IGVFFI9608CCLH/), [IGVFFI2013KLCS](/sequence-files/IGVFFI2013KLCS/), [IGVFFI3590RFFA](/sequence-files/IGVFFI3590RFFA/), [IGVFFI4064LQPH](/sequence-files/IGVFFI4064LQPH/), [IGVFFI8614YIIT](/sequence-files/IGVFFI8614YIIT/), [IGVFFI4224TVST](/sequence-files/IGVFFI4224TVST/), [IGVFFI4196IBSF](/sequence-files/IGVFFI4196IBSF/), [IGVFFI2720CWNA](/sequence-files/IGVFFI2720CWNA/), [IGVFFI6885RUCL](/sequence-files/IGVFFI6885RUCL/), [IGVFFI2362JMED](/sequence-files/IGVFFI2362JMED/) 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/IGVFDS1470QEOX/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1470QEOX](/auxiliary-sets/IGVFDS1470QEOX/) 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/IGVFDS1470QEOX/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1470QEOX/",
"accession": "IGVFDS1470QEOX",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-BinB_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": "2023-12-13T08:48:06.644925+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": "2023-12-20T23:08:53.303539+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1838USXI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1838USXI",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-BinB"
],
"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 26-50% 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": "2023-12-13T09:44:31.202108+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": "486481b8-27b4-4eef-96cd-a835536b000a"
}