{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2388VNTG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2388VNTG",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-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 [IGVFSM2021SEKU](/in-vitro-systems/IGVFSM2021SEKU/) 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/IGVFSM2021SEKU/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2388VNTG](/measurement-sets/IGVFDS2388VNTG/) has in progress subobject auxiliary set [IGVFDS8378MWDI](/auxiliary-sets/IGVFDS8378MWDI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2388VNTG/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8378MWDI](/auxiliary-sets/IGVFDS8378MWDI/) has sequence file(s): [IGVFFI3689QEEW](/sequence-files/IGVFFI3689QEEW/), [IGVFFI1617ZUZD](/sequence-files/IGVFFI1617ZUZD/), [IGVFFI1255KULZ](/sequence-files/IGVFFI1255KULZ/), [IGVFFI4127MRWO](/sequence-files/IGVFFI4127MRWO/), [IGVFFI0219UGYW](/sequence-files/IGVFFI0219UGYW/), [IGVFFI0669PTDU](/sequence-files/IGVFFI0669PTDU/), [IGVFFI5521TKSC](/sequence-files/IGVFFI5521TKSC/), [IGVFFI3483BWBI](/sequence-files/IGVFFI3483BWBI/), [IGVFFI7153IFKZ](/sequence-files/IGVFFI7153IFKZ/), [IGVFFI9094KSLB](/sequence-files/IGVFFI9094KSLB/), [IGVFFI2242TUEN](/sequence-files/IGVFFI2242TUEN/), [IGVFFI3707KINU](/sequence-files/IGVFFI3707KINU/), [IGVFFI9017IJDC](/sequence-files/IGVFFI9017IJDC/), [IGVFFI2021BJMY](/sequence-files/IGVFFI2021BJMY/), [IGVFFI5684TJHR](/sequence-files/IGVFFI5684TJHR/), [IGVFFI7030MTMP](/sequence-files/IGVFFI7030MTMP/), [IGVFFI1873UYVI](/sequence-files/IGVFFI1873UYVI/), [IGVFFI0599DXQV](/sequence-files/IGVFFI0599DXQV/), [IGVFFI3690OMJM](/sequence-files/IGVFFI3690OMJM/), [IGVFFI5383EEXJ](/sequence-files/IGVFFI5383EEXJ/), [IGVFFI6884RFEC](/sequence-files/IGVFFI6884RFEC/), [IGVFFI1572ACWX](/sequence-files/IGVFFI1572ACWX/), [IGVFFI6992PQWV](/sequence-files/IGVFFI6992PQWV/), [IGVFFI8415DQDR](/sequence-files/IGVFFI8415DQDR/), [IGVFFI5639JXZV](/sequence-files/IGVFFI5639JXZV/), [IGVFFI6978YTCX](/sequence-files/IGVFFI6978YTCX/), [IGVFFI8571QVSM](/sequence-files/IGVFFI8571QVSM/), [IGVFFI9129AOAE](/sequence-files/IGVFFI9129AOAE/), [IGVFFI6542LODF](/sequence-files/IGVFFI6542LODF/), [IGVFFI1161HAWR](/sequence-files/IGVFFI1161HAWR/), [IGVFFI7884BTIT](/sequence-files/IGVFFI7884BTIT/), [IGVFFI8544AUIF](/sequence-files/IGVFFI8544AUIF/), [IGVFFI8780SAIX](/sequence-files/IGVFFI8780SAIX/), [IGVFFI0797HGEV](/sequence-files/IGVFFI0797HGEV/), [IGVFFI5500RJZS](/sequence-files/IGVFFI5500RJZS/), [IGVFFI9648RTAF](/sequence-files/IGVFFI9648RTAF/), [IGVFFI1760KIKE](/sequence-files/IGVFFI1760KIKE/), [IGVFFI3509PPFA](/sequence-files/IGVFFI3509PPFA/), [IGVFFI6890BDEA](/sequence-files/IGVFFI6890BDEA/), [IGVFFI3315NOSZ](/sequence-files/IGVFFI3315NOSZ/), [IGVFFI1205IAWO](/sequence-files/IGVFFI1205IAWO/), [IGVFFI3945LGUG](/sequence-files/IGVFFI3945LGUG/), [IGVFFI2212ECCZ](/sequence-files/IGVFFI2212ECCZ/), [IGVFFI9712UYUV](/sequence-files/IGVFFI9712UYUV/), [IGVFFI7913MSIY](/sequence-files/IGVFFI7913MSIY/), [IGVFFI6055FGKO](/sequence-files/IGVFFI6055FGKO/), [IGVFFI9616IDJP](/sequence-files/IGVFFI9616IDJP/), [IGVFFI6518NQZE](/sequence-files/IGVFFI6518NQZE/) 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/IGVFDS8378MWDI/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2388VNTG](/measurement-sets/IGVFDS2388VNTG/) 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/IGVFDS2388VNTG/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8378MWDI](/auxiliary-sets/IGVFDS8378MWDI/) has sequence file(s) [IGVFFI3689QEEW](/sequence-files/IGVFFI3689QEEW/), [IGVFFI1617ZUZD](/sequence-files/IGVFFI1617ZUZD/), [IGVFFI1255KULZ](/sequence-files/IGVFFI1255KULZ/), [IGVFFI4127MRWO](/sequence-files/IGVFFI4127MRWO/), [IGVFFI0219UGYW](/sequence-files/IGVFFI0219UGYW/), [IGVFFI0669PTDU](/sequence-files/IGVFFI0669PTDU/), [IGVFFI5521TKSC](/sequence-files/IGVFFI5521TKSC/), [IGVFFI3483BWBI](/sequence-files/IGVFFI3483BWBI/), [IGVFFI7153IFKZ](/sequence-files/IGVFFI7153IFKZ/), [IGVFFI9094KSLB](/sequence-files/IGVFFI9094KSLB/), [IGVFFI2242TUEN](/sequence-files/IGVFFI2242TUEN/), [IGVFFI3707KINU](/sequence-files/IGVFFI3707KINU/), [IGVFFI9017IJDC](/sequence-files/IGVFFI9017IJDC/), [IGVFFI2021BJMY](/sequence-files/IGVFFI2021BJMY/), [IGVFFI5684TJHR](/sequence-files/IGVFFI5684TJHR/), [IGVFFI7030MTMP](/sequence-files/IGVFFI7030MTMP/), [IGVFFI1873UYVI](/sequence-files/IGVFFI1873UYVI/), [IGVFFI0599DXQV](/sequence-files/IGVFFI0599DXQV/), [IGVFFI3690OMJM](/sequence-files/IGVFFI3690OMJM/), [IGVFFI5383EEXJ](/sequence-files/IGVFFI5383EEXJ/), [IGVFFI6884RFEC](/sequence-files/IGVFFI6884RFEC/), [IGVFFI1572ACWX](/sequence-files/IGVFFI1572ACWX/), [IGVFFI6992PQWV](/sequence-files/IGVFFI6992PQWV/), [IGVFFI8415DQDR](/sequence-files/IGVFFI8415DQDR/), [IGVFFI5639JXZV](/sequence-files/IGVFFI5639JXZV/), [IGVFFI6978YTCX](/sequence-files/IGVFFI6978YTCX/), [IGVFFI8571QVSM](/sequence-files/IGVFFI8571QVSM/), [IGVFFI9129AOAE](/sequence-files/IGVFFI9129AOAE/), [IGVFFI6542LODF](/sequence-files/IGVFFI6542LODF/), [IGVFFI1161HAWR](/sequence-files/IGVFFI1161HAWR/), [IGVFFI7884BTIT](/sequence-files/IGVFFI7884BTIT/), [IGVFFI8544AUIF](/sequence-files/IGVFFI8544AUIF/), [IGVFFI8780SAIX](/sequence-files/IGVFFI8780SAIX/), [IGVFFI0797HGEV](/sequence-files/IGVFFI0797HGEV/), [IGVFFI5500RJZS](/sequence-files/IGVFFI5500RJZS/), [IGVFFI9648RTAF](/sequence-files/IGVFFI9648RTAF/), [IGVFFI1760KIKE](/sequence-files/IGVFFI1760KIKE/), [IGVFFI3509PPFA](/sequence-files/IGVFFI3509PPFA/), [IGVFFI6890BDEA](/sequence-files/IGVFFI6890BDEA/), [IGVFFI3315NOSZ](/sequence-files/IGVFFI3315NOSZ/), [IGVFFI1205IAWO](/sequence-files/IGVFFI1205IAWO/), [IGVFFI3945LGUG](/sequence-files/IGVFFI3945LGUG/), [IGVFFI2212ECCZ](/sequence-files/IGVFFI2212ECCZ/), [IGVFFI9712UYUV](/sequence-files/IGVFFI9712UYUV/), [IGVFFI7913MSIY](/sequence-files/IGVFFI7913MSIY/), [IGVFFI6055FGKO](/sequence-files/IGVFFI6055FGKO/), [IGVFFI9616IDJP](/sequence-files/IGVFFI9616IDJP/), [IGVFFI6518NQZE](/sequence-files/IGVFFI6518NQZE/) 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/IGVFDS8378MWDI/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8378MWDI](/auxiliary-sets/IGVFDS8378MWDI/) 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/IGVFDS8378MWDI/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8378MWDI/",
"accession": "IGVFDS8378MWDI",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-13T08:48:10.481419+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": "2023-12-20T23:08:54.784386+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2021SEKU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2021SEKU",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-13T10:00:44.222465+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": "d0e6b481-427c-41bb-9743-bb53eb2c38fd"
}