{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8947TZOV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8947TZOV",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-BinB_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 [IGVFDS8947TZOV](/measurement-sets/IGVFDS8947TZOV/) has sequence file(s) [IGVFFI1734LMPY](/sequence-files/IGVFFI1734LMPY/), [IGVFFI3226RILR](/sequence-files/IGVFFI3226RILR/), [IGVFFI8511PQAK](/sequence-files/IGVFFI8511PQAK/), [IGVFFI3441BDRO](/sequence-files/IGVFFI3441BDRO/), [IGVFFI0836QGBC](/sequence-files/IGVFFI0836QGBC/), [IGVFFI8234VYDY](/sequence-files/IGVFFI8234VYDY/), [IGVFFI4050YOBY](/sequence-files/IGVFFI4050YOBY/), [IGVFFI1890JZHP](/sequence-files/IGVFFI1890JZHP/), [IGVFFI3759BUVD](/sequence-files/IGVFFI3759BUVD/), [IGVFFI0227KJFH](/sequence-files/IGVFFI0227KJFH/), [IGVFFI7241NJVG](/sequence-files/IGVFFI7241NJVG/), [IGVFFI1688JOFP](/sequence-files/IGVFFI1688JOFP/), [IGVFFI8059UICA](/sequence-files/IGVFFI8059UICA/), [IGVFFI3515NRCF](/sequence-files/IGVFFI3515NRCF/), [IGVFFI1441QXAR](/sequence-files/IGVFFI1441QXAR/), [IGVFFI8762LXMI](/sequence-files/IGVFFI8762LXMI/), [IGVFFI7386QJTU](/sequence-files/IGVFFI7386QJTU/), [IGVFFI5900MYSK](/sequence-files/IGVFFI5900MYSK/), [IGVFFI2641YHBQ](/sequence-files/IGVFFI2641YHBQ/), [IGVFFI3773RQPU](/sequence-files/IGVFFI3773RQPU/), [IGVFFI0272TOWM](/sequence-files/IGVFFI0272TOWM/), [IGVFFI0881GMDN](/sequence-files/IGVFFI0881GMDN/), [IGVFFI3146XBHC](/sequence-files/IGVFFI3146XBHC/), [IGVFFI8334FCDG](/sequence-files/IGVFFI8334FCDG/), [IGVFFI7849RVXS](/sequence-files/IGVFFI7849RVXS/), [IGVFFI3621NRQN](/sequence-files/IGVFFI3621NRQN/), [IGVFFI3194HHLC](/sequence-files/IGVFFI3194HHLC/), [IGVFFI4142YPUY](/sequence-files/IGVFFI4142YPUY/), [IGVFFI9950VRZC](/sequence-files/IGVFFI9950VRZC/), [IGVFFI6098UPUP](/sequence-files/IGVFFI6098UPUP/), [IGVFFI6882AYLU](/sequence-files/IGVFFI6882AYLU/), [IGVFFI8623XECF](/sequence-files/IGVFFI8623XECF/), [IGVFFI3822KMIU](/sequence-files/IGVFFI3822KMIU/), [IGVFFI3872LEHB](/sequence-files/IGVFFI3872LEHB/), [IGVFFI6143KOGY](/sequence-files/IGVFFI6143KOGY/), [IGVFFI0724UPKW](/sequence-files/IGVFFI0724UPKW/), [IGVFFI6003FUTQ](/sequence-files/IGVFFI6003FUTQ/), [IGVFFI7402XEWR](/sequence-files/IGVFFI7402XEWR/), [IGVFFI7819VOXZ](/sequence-files/IGVFFI7819VOXZ/), [IGVFFI1451MCYO](/sequence-files/IGVFFI1451MCYO/), [IGVFFI2792BXFU](/sequence-files/IGVFFI2792BXFU/), [IGVFFI8248MPUQ](/sequence-files/IGVFFI8248MPUQ/), [IGVFFI1673QSGK](/sequence-files/IGVFFI1673QSGK/), [IGVFFI9101UBHG](/sequence-files/IGVFFI9101UBHG/), [IGVFFI7328ZZGN](/sequence-files/IGVFFI7328ZZGN/), [IGVFFI6659SAFD](/sequence-files/IGVFFI6659SAFD/), [IGVFFI2480AFEX](/sequence-files/IGVFFI2480AFEX/), [IGVFFI4043PDDC](/sequence-files/IGVFFI4043PDDC/) 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/IGVFDS8947TZOV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8947TZOV](/measurement-sets/IGVFDS8947TZOV/) has sequence file(s): [IGVFFI1734LMPY](/sequence-files/IGVFFI1734LMPY/), [IGVFFI3226RILR](/sequence-files/IGVFFI3226RILR/), [IGVFFI8511PQAK](/sequence-files/IGVFFI8511PQAK/), [IGVFFI3441BDRO](/sequence-files/IGVFFI3441BDRO/), [IGVFFI0836QGBC](/sequence-files/IGVFFI0836QGBC/), [IGVFFI8234VYDY](/sequence-files/IGVFFI8234VYDY/), [IGVFFI4050YOBY](/sequence-files/IGVFFI4050YOBY/), [IGVFFI1890JZHP](/sequence-files/IGVFFI1890JZHP/), [IGVFFI3759BUVD](/sequence-files/IGVFFI3759BUVD/), [IGVFFI0227KJFH](/sequence-files/IGVFFI0227KJFH/), [IGVFFI7241NJVG](/sequence-files/IGVFFI7241NJVG/), [IGVFFI1688JOFP](/sequence-files/IGVFFI1688JOFP/), [IGVFFI8059UICA](/sequence-files/IGVFFI8059UICA/), [IGVFFI3515NRCF](/sequence-files/IGVFFI3515NRCF/), [IGVFFI1441QXAR](/sequence-files/IGVFFI1441QXAR/), [IGVFFI8762LXMI](/sequence-files/IGVFFI8762LXMI/), [IGVFFI7386QJTU](/sequence-files/IGVFFI7386QJTU/), [IGVFFI5900MYSK](/sequence-files/IGVFFI5900MYSK/), [IGVFFI2641YHBQ](/sequence-files/IGVFFI2641YHBQ/), [IGVFFI3773RQPU](/sequence-files/IGVFFI3773RQPU/), [IGVFFI0272TOWM](/sequence-files/IGVFFI0272TOWM/), [IGVFFI0881GMDN](/sequence-files/IGVFFI0881GMDN/), [IGVFFI3146XBHC](/sequence-files/IGVFFI3146XBHC/), [IGVFFI8334FCDG](/sequence-files/IGVFFI8334FCDG/), [IGVFFI7849RVXS](/sequence-files/IGVFFI7849RVXS/), [IGVFFI3621NRQN](/sequence-files/IGVFFI3621NRQN/), [IGVFFI3194HHLC](/sequence-files/IGVFFI3194HHLC/), [IGVFFI4142YPUY](/sequence-files/IGVFFI4142YPUY/), [IGVFFI9950VRZC](/sequence-files/IGVFFI9950VRZC/), [IGVFFI6098UPUP](/sequence-files/IGVFFI6098UPUP/), [IGVFFI6882AYLU](/sequence-files/IGVFFI6882AYLU/), [IGVFFI8623XECF](/sequence-files/IGVFFI8623XECF/), [IGVFFI3822KMIU](/sequence-files/IGVFFI3822KMIU/), [IGVFFI3872LEHB](/sequence-files/IGVFFI3872LEHB/), [IGVFFI6143KOGY](/sequence-files/IGVFFI6143KOGY/), [IGVFFI0724UPKW](/sequence-files/IGVFFI0724UPKW/), [IGVFFI6003FUTQ](/sequence-files/IGVFFI6003FUTQ/), [IGVFFI7402XEWR](/sequence-files/IGVFFI7402XEWR/), [IGVFFI7819VOXZ](/sequence-files/IGVFFI7819VOXZ/), [IGVFFI1451MCYO](/sequence-files/IGVFFI1451MCYO/), [IGVFFI2792BXFU](/sequence-files/IGVFFI2792BXFU/), [IGVFFI8248MPUQ](/sequence-files/IGVFFI8248MPUQ/), [IGVFFI1673QSGK](/sequence-files/IGVFFI1673QSGK/), [IGVFFI9101UBHG](/sequence-files/IGVFFI9101UBHG/), [IGVFFI7328ZZGN](/sequence-files/IGVFFI7328ZZGN/), [IGVFFI6659SAFD](/sequence-files/IGVFFI6659SAFD/), [IGVFFI2480AFEX](/sequence-files/IGVFFI2480AFEX/), [IGVFFI4043PDDC](/sequence-files/IGVFFI4043PDDC/) 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/IGVFDS8947TZOV/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8947TZOV](/measurement-sets/IGVFDS8947TZOV/) 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/IGVFDS8947TZOV/"
}
]
},
"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": "2024-11-25T23:52:48.138181+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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},
{
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},
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},
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},
{
"@id": "/sequence-files/IGVFFI7241NJVG/",
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],
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"@id": "/construct-library-sets/IGVFDS4955GEYO/",
"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 26-50% 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": "2024-11-26T06:40:48.153067+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": "e6d41c4a-7ea9-4b32-bc8e-812a454bb480"
}