{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5752WCRU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5752WCRU",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5752WCRU](/measurement-sets/IGVFDS5752WCRU/) has sequence file(s) [IGVFFI8941FHLN](/sequence-files/IGVFFI8941FHLN/), [IGVFFI7063EOFS](/sequence-files/IGVFFI7063EOFS/), [IGVFFI6276FRYO](/sequence-files/IGVFFI6276FRYO/), [IGVFFI9576IXOX](/sequence-files/IGVFFI9576IXOX/), [IGVFFI4522QWFP](/sequence-files/IGVFFI4522QWFP/), [IGVFFI7191NJRV](/sequence-files/IGVFFI7191NJRV/), [IGVFFI5644VYAQ](/sequence-files/IGVFFI5644VYAQ/), [IGVFFI4188FQQB](/sequence-files/IGVFFI4188FQQB/), [IGVFFI2732DOXD](/sequence-files/IGVFFI2732DOXD/), [IGVFFI3892BLTR](/sequence-files/IGVFFI3892BLTR/), [IGVFFI2501VREN](/sequence-files/IGVFFI2501VREN/), [IGVFFI3999OBGE](/sequence-files/IGVFFI3999OBGE/), [IGVFFI8684YABG](/sequence-files/IGVFFI8684YABG/), [IGVFFI5580YWXA](/sequence-files/IGVFFI5580YWXA/), [IGVFFI1263DKDS](/sequence-files/IGVFFI1263DKDS/), [IGVFFI1893VFYB](/sequence-files/IGVFFI1893VFYB/), [IGVFFI3454JLFG](/sequence-files/IGVFFI3454JLFG/), [IGVFFI9815YIID](/sequence-files/IGVFFI9815YIID/), [IGVFFI3933ZUOL](/sequence-files/IGVFFI3933ZUOL/), [IGVFFI5265VEFY](/sequence-files/IGVFFI5265VEFY/), [IGVFFI4297WMUV](/sequence-files/IGVFFI4297WMUV/), [IGVFFI4885XJAR](/sequence-files/IGVFFI4885XJAR/), [IGVFFI0908OOTX](/sequence-files/IGVFFI0908OOTX/), [IGVFFI6032HNPE](/sequence-files/IGVFFI6032HNPE/), [IGVFFI5960ZCDP](/sequence-files/IGVFFI5960ZCDP/), [IGVFFI4774SGQO](/sequence-files/IGVFFI4774SGQO/), [IGVFFI0150PRYU](/sequence-files/IGVFFI0150PRYU/), [IGVFFI1236KEYQ](/sequence-files/IGVFFI1236KEYQ/), [IGVFFI0372KWJH](/sequence-files/IGVFFI0372KWJH/), [IGVFFI8053BGTW](/sequence-files/IGVFFI8053BGTW/), [IGVFFI2646CXDP](/sequence-files/IGVFFI2646CXDP/), [IGVFFI3422DMRD](/sequence-files/IGVFFI3422DMRD/), [IGVFFI1790KNJY](/sequence-files/IGVFFI1790KNJY/), [IGVFFI3233JWYV](/sequence-files/IGVFFI3233JWYV/), [IGVFFI3309NVTO](/sequence-files/IGVFFI3309NVTO/), [IGVFFI5457BEBR](/sequence-files/IGVFFI5457BEBR/), [IGVFFI8444HAPQ](/sequence-files/IGVFFI8444HAPQ/), [IGVFFI5951DCNI](/sequence-files/IGVFFI5951DCNI/), [IGVFFI8305YRWN](/sequence-files/IGVFFI8305YRWN/), [IGVFFI7787PEMK](/sequence-files/IGVFFI7787PEMK/), [IGVFFI3756LRPM](/sequence-files/IGVFFI3756LRPM/), [IGVFFI2194ETYQ](/sequence-files/IGVFFI2194ETYQ/), [IGVFFI4482FCWE](/sequence-files/IGVFFI4482FCWE/), [IGVFFI0577IBTP](/sequence-files/IGVFFI0577IBTP/), [IGVFFI5785XJEW](/sequence-files/IGVFFI5785XJEW/), [IGVFFI2593VOVB](/sequence-files/IGVFFI2593VOVB/), [IGVFFI5477AQIH](/sequence-files/IGVFFI5477AQIH/), [IGVFFI1590OQWL](/sequence-files/IGVFFI1590OQWL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS5752WCRU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5752WCRU](/measurement-sets/IGVFDS5752WCRU/) has sequence file(s): [IGVFFI8941FHLN](/sequence-files/IGVFFI8941FHLN/), [IGVFFI7063EOFS](/sequence-files/IGVFFI7063EOFS/), [IGVFFI6276FRYO](/sequence-files/IGVFFI6276FRYO/), [IGVFFI9576IXOX](/sequence-files/IGVFFI9576IXOX/), [IGVFFI4522QWFP](/sequence-files/IGVFFI4522QWFP/), [IGVFFI7191NJRV](/sequence-files/IGVFFI7191NJRV/), [IGVFFI5644VYAQ](/sequence-files/IGVFFI5644VYAQ/), [IGVFFI4188FQQB](/sequence-files/IGVFFI4188FQQB/), [IGVFFI2732DOXD](/sequence-files/IGVFFI2732DOXD/), [IGVFFI3892BLTR](/sequence-files/IGVFFI3892BLTR/), [IGVFFI2501VREN](/sequence-files/IGVFFI2501VREN/), [IGVFFI3999OBGE](/sequence-files/IGVFFI3999OBGE/), [IGVFFI8684YABG](/sequence-files/IGVFFI8684YABG/), [IGVFFI5580YWXA](/sequence-files/IGVFFI5580YWXA/), [IGVFFI1263DKDS](/sequence-files/IGVFFI1263DKDS/), [IGVFFI1893VFYB](/sequence-files/IGVFFI1893VFYB/), [IGVFFI3454JLFG](/sequence-files/IGVFFI3454JLFG/), [IGVFFI9815YIID](/sequence-files/IGVFFI9815YIID/), [IGVFFI3933ZUOL](/sequence-files/IGVFFI3933ZUOL/), [IGVFFI5265VEFY](/sequence-files/IGVFFI5265VEFY/), [IGVFFI4297WMUV](/sequence-files/IGVFFI4297WMUV/), [IGVFFI4885XJAR](/sequence-files/IGVFFI4885XJAR/), [IGVFFI0908OOTX](/sequence-files/IGVFFI0908OOTX/), [IGVFFI6032HNPE](/sequence-files/IGVFFI6032HNPE/), [IGVFFI5960ZCDP](/sequence-files/IGVFFI5960ZCDP/), [IGVFFI4774SGQO](/sequence-files/IGVFFI4774SGQO/), [IGVFFI0150PRYU](/sequence-files/IGVFFI0150PRYU/), [IGVFFI1236KEYQ](/sequence-files/IGVFFI1236KEYQ/), [IGVFFI0372KWJH](/sequence-files/IGVFFI0372KWJH/), [IGVFFI8053BGTW](/sequence-files/IGVFFI8053BGTW/), [IGVFFI2646CXDP](/sequence-files/IGVFFI2646CXDP/), [IGVFFI3422DMRD](/sequence-files/IGVFFI3422DMRD/), [IGVFFI1790KNJY](/sequence-files/IGVFFI1790KNJY/), [IGVFFI3233JWYV](/sequence-files/IGVFFI3233JWYV/), [IGVFFI3309NVTO](/sequence-files/IGVFFI3309NVTO/), [IGVFFI5457BEBR](/sequence-files/IGVFFI5457BEBR/), [IGVFFI8444HAPQ](/sequence-files/IGVFFI8444HAPQ/), [IGVFFI5951DCNI](/sequence-files/IGVFFI5951DCNI/), [IGVFFI8305YRWN](/sequence-files/IGVFFI8305YRWN/), [IGVFFI7787PEMK](/sequence-files/IGVFFI7787PEMK/), [IGVFFI3756LRPM](/sequence-files/IGVFFI3756LRPM/), [IGVFFI2194ETYQ](/sequence-files/IGVFFI2194ETYQ/), [IGVFFI4482FCWE](/sequence-files/IGVFFI4482FCWE/), [IGVFFI0577IBTP](/sequence-files/IGVFFI0577IBTP/), [IGVFFI5785XJEW](/sequence-files/IGVFFI5785XJEW/), [IGVFFI2593VOVB](/sequence-files/IGVFFI2593VOVB/), [IGVFFI5477AQIH](/sequence-files/IGVFFI5477AQIH/), [IGVFFI1590OQWL](/sequence-files/IGVFFI1590OQWL/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS5752WCRU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5752WCRU](/measurement-sets/IGVFDS5752WCRU/) 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": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS5752WCRU/"
}
]
},
"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"
},
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{
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"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:53:12.877589+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
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},
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"accession": "IGVFDS4955GEYO",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-26T06:55:44.955383+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"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": "eeef85bf-df17-45c7-b823-b8f358819ac1"
}