{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0061JZWG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0061JZWG",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-BinD_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 [IGVFSM4672UCMH](/in-vitro-systems/IGVFSM4672UCMH/) 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/IGVFSM4672UCMH/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0061JZWG](/measurement-sets/IGVFDS0061JZWG/) has in progress subobject auxiliary set [IGVFDS2275YFPM](/auxiliary-sets/IGVFDS2275YFPM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0061JZWG/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0061JZWG](/measurement-sets/IGVFDS0061JZWG/) 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/IGVFDS0061JZWG/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2275YFPM](/auxiliary-sets/IGVFDS2275YFPM/) has sequence file(s): [IGVFFI2393DVPQ](/sequence-files/IGVFFI2393DVPQ/), [IGVFFI9653EQGJ](/sequence-files/IGVFFI9653EQGJ/), [IGVFFI2132AZNM](/sequence-files/IGVFFI2132AZNM/), [IGVFFI4119LHRK](/sequence-files/IGVFFI4119LHRK/), [IGVFFI2214QULM](/sequence-files/IGVFFI2214QULM/), [IGVFFI6080FVHM](/sequence-files/IGVFFI6080FVHM/), [IGVFFI9326XZQX](/sequence-files/IGVFFI9326XZQX/), [IGVFFI9865DPAE](/sequence-files/IGVFFI9865DPAE/), [IGVFFI6642FMQM](/sequence-files/IGVFFI6642FMQM/), [IGVFFI6352COBS](/sequence-files/IGVFFI6352COBS/), [IGVFFI8722DOQH](/sequence-files/IGVFFI8722DOQH/), [IGVFFI8572WUST](/sequence-files/IGVFFI8572WUST/), [IGVFFI2492HRRN](/sequence-files/IGVFFI2492HRRN/), [IGVFFI9808IRFZ](/sequence-files/IGVFFI9808IRFZ/), [IGVFFI9187UKUN](/sequence-files/IGVFFI9187UKUN/), [IGVFFI1260OBFY](/sequence-files/IGVFFI1260OBFY/), [IGVFFI7333KWAJ](/sequence-files/IGVFFI7333KWAJ/), [IGVFFI1045MCNC](/sequence-files/IGVFFI1045MCNC/), [IGVFFI7850RJGK](/sequence-files/IGVFFI7850RJGK/), [IGVFFI8630QHVD](/sequence-files/IGVFFI8630QHVD/), [IGVFFI9029QALN](/sequence-files/IGVFFI9029QALN/), [IGVFFI6967OLFO](/sequence-files/IGVFFI6967OLFO/), [IGVFFI8548WMTT](/sequence-files/IGVFFI8548WMTT/), [IGVFFI7420HOZP](/sequence-files/IGVFFI7420HOZP/), [IGVFFI0820GWDT](/sequence-files/IGVFFI0820GWDT/), [IGVFFI5578XQCE](/sequence-files/IGVFFI5578XQCE/), [IGVFFI9671LJAH](/sequence-files/IGVFFI9671LJAH/), [IGVFFI9582NMEI](/sequence-files/IGVFFI9582NMEI/), [IGVFFI9156MCIG](/sequence-files/IGVFFI9156MCIG/), [IGVFFI8423DEHL](/sequence-files/IGVFFI8423DEHL/), [IGVFFI6504FRHJ](/sequence-files/IGVFFI6504FRHJ/), [IGVFFI6838QSXC](/sequence-files/IGVFFI6838QSXC/), [IGVFFI7224HFUK](/sequence-files/IGVFFI7224HFUK/), [IGVFFI3295GQWP](/sequence-files/IGVFFI3295GQWP/), [IGVFFI0394TMBX](/sequence-files/IGVFFI0394TMBX/), [IGVFFI5016ZELF](/sequence-files/IGVFFI5016ZELF/), [IGVFFI0227JVVV](/sequence-files/IGVFFI0227JVVV/), [IGVFFI9512LKZW](/sequence-files/IGVFFI9512LKZW/), [IGVFFI6170ZNSB](/sequence-files/IGVFFI6170ZNSB/), [IGVFFI9664YGHG](/sequence-files/IGVFFI9664YGHG/), [IGVFFI3032TRJZ](/sequence-files/IGVFFI3032TRJZ/), [IGVFFI4150CIBP](/sequence-files/IGVFFI4150CIBP/), [IGVFFI0930NSXB](/sequence-files/IGVFFI0930NSXB/), [IGVFFI5655DBXU](/sequence-files/IGVFFI5655DBXU/), [IGVFFI5153NXCU](/sequence-files/IGVFFI5153NXCU/), [IGVFFI9129ZJLL](/sequence-files/IGVFFI9129ZJLL/), [IGVFFI0834TCAU](/sequence-files/IGVFFI0834TCAU/), [IGVFFI7502YUHA](/sequence-files/IGVFFI7502YUHA/) 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/IGVFDS2275YFPM/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2275YFPM](/auxiliary-sets/IGVFDS2275YFPM/) has sequence file(s) [IGVFFI2393DVPQ](/sequence-files/IGVFFI2393DVPQ/), [IGVFFI9653EQGJ](/sequence-files/IGVFFI9653EQGJ/), [IGVFFI2132AZNM](/sequence-files/IGVFFI2132AZNM/), [IGVFFI4119LHRK](/sequence-files/IGVFFI4119LHRK/), [IGVFFI2214QULM](/sequence-files/IGVFFI2214QULM/), [IGVFFI6080FVHM](/sequence-files/IGVFFI6080FVHM/), [IGVFFI9326XZQX](/sequence-files/IGVFFI9326XZQX/), [IGVFFI9865DPAE](/sequence-files/IGVFFI9865DPAE/), [IGVFFI6642FMQM](/sequence-files/IGVFFI6642FMQM/), [IGVFFI6352COBS](/sequence-files/IGVFFI6352COBS/), [IGVFFI8722DOQH](/sequence-files/IGVFFI8722DOQH/), [IGVFFI8572WUST](/sequence-files/IGVFFI8572WUST/), [IGVFFI2492HRRN](/sequence-files/IGVFFI2492HRRN/), [IGVFFI9808IRFZ](/sequence-files/IGVFFI9808IRFZ/), [IGVFFI9187UKUN](/sequence-files/IGVFFI9187UKUN/), [IGVFFI1260OBFY](/sequence-files/IGVFFI1260OBFY/), [IGVFFI7333KWAJ](/sequence-files/IGVFFI7333KWAJ/), [IGVFFI1045MCNC](/sequence-files/IGVFFI1045MCNC/), [IGVFFI7850RJGK](/sequence-files/IGVFFI7850RJGK/), [IGVFFI8630QHVD](/sequence-files/IGVFFI8630QHVD/), [IGVFFI9029QALN](/sequence-files/IGVFFI9029QALN/), [IGVFFI6967OLFO](/sequence-files/IGVFFI6967OLFO/), [IGVFFI8548WMTT](/sequence-files/IGVFFI8548WMTT/), [IGVFFI7420HOZP](/sequence-files/IGVFFI7420HOZP/), [IGVFFI0820GWDT](/sequence-files/IGVFFI0820GWDT/), [IGVFFI5578XQCE](/sequence-files/IGVFFI5578XQCE/), [IGVFFI9671LJAH](/sequence-files/IGVFFI9671LJAH/), [IGVFFI9582NMEI](/sequence-files/IGVFFI9582NMEI/), [IGVFFI9156MCIG](/sequence-files/IGVFFI9156MCIG/), [IGVFFI8423DEHL](/sequence-files/IGVFFI8423DEHL/), [IGVFFI6504FRHJ](/sequence-files/IGVFFI6504FRHJ/), [IGVFFI6838QSXC](/sequence-files/IGVFFI6838QSXC/), [IGVFFI7224HFUK](/sequence-files/IGVFFI7224HFUK/), [IGVFFI3295GQWP](/sequence-files/IGVFFI3295GQWP/), [IGVFFI0394TMBX](/sequence-files/IGVFFI0394TMBX/), [IGVFFI5016ZELF](/sequence-files/IGVFFI5016ZELF/), [IGVFFI0227JVVV](/sequence-files/IGVFFI0227JVVV/), [IGVFFI9512LKZW](/sequence-files/IGVFFI9512LKZW/), [IGVFFI6170ZNSB](/sequence-files/IGVFFI6170ZNSB/), [IGVFFI9664YGHG](/sequence-files/IGVFFI9664YGHG/), [IGVFFI3032TRJZ](/sequence-files/IGVFFI3032TRJZ/), [IGVFFI4150CIBP](/sequence-files/IGVFFI4150CIBP/), [IGVFFI0930NSXB](/sequence-files/IGVFFI0930NSXB/), [IGVFFI5655DBXU](/sequence-files/IGVFFI5655DBXU/), [IGVFFI5153NXCU](/sequence-files/IGVFFI5153NXCU/), [IGVFFI9129ZJLL](/sequence-files/IGVFFI9129ZJLL/), [IGVFFI0834TCAU](/sequence-files/IGVFFI0834TCAU/), [IGVFFI7502YUHA](/sequence-files/IGVFFI7502YUHA/) 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/IGVFDS2275YFPM/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2275YFPM](/auxiliary-sets/IGVFDS2275YFPM/) 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/IGVFDS2275YFPM/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2275YFPM/",
"accession": "IGVFDS2275YFPM",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-BinD_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": "2023-12-13T08:48:14.248156+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": "2023-12-20T23:08:33.271510+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4672UCMH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4672UCMH",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-BinD"
],
"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 76-100% 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": "2023-12-13T10:16:51.053538+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": "96f36ea9-0e2b-4aae-a55e-69ec7c23995f"
}