{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9127RZLI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9127RZLI",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-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 [IGVFDS9127RZLI](/measurement-sets/IGVFDS9127RZLI/) has sequence file(s) [IGVFFI5174DBSG](/sequence-files/IGVFFI5174DBSG/), [IGVFFI6843MNDS](/sequence-files/IGVFFI6843MNDS/), [IGVFFI3922VCPP](/sequence-files/IGVFFI3922VCPP/), [IGVFFI4085QSPN](/sequence-files/IGVFFI4085QSPN/), [IGVFFI1423UTDZ](/sequence-files/IGVFFI1423UTDZ/), [IGVFFI0799ZPYK](/sequence-files/IGVFFI0799ZPYK/), [IGVFFI3487CNKY](/sequence-files/IGVFFI3487CNKY/), [IGVFFI3485NRKR](/sequence-files/IGVFFI3485NRKR/), [IGVFFI8197IMOS](/sequence-files/IGVFFI8197IMOS/), [IGVFFI3339JEGG](/sequence-files/IGVFFI3339JEGG/), [IGVFFI4948ONLC](/sequence-files/IGVFFI4948ONLC/), [IGVFFI5434NZLG](/sequence-files/IGVFFI5434NZLG/), [IGVFFI8147DKKP](/sequence-files/IGVFFI8147DKKP/), [IGVFFI1776BCXZ](/sequence-files/IGVFFI1776BCXZ/), [IGVFFI7884POCN](/sequence-files/IGVFFI7884POCN/), [IGVFFI0281YRYH](/sequence-files/IGVFFI0281YRYH/), [IGVFFI1446TUPZ](/sequence-files/IGVFFI1446TUPZ/), [IGVFFI8373MHJM](/sequence-files/IGVFFI8373MHJM/), [IGVFFI2924KQZD](/sequence-files/IGVFFI2924KQZD/), [IGVFFI3319ZLNA](/sequence-files/IGVFFI3319ZLNA/), [IGVFFI1689RHYO](/sequence-files/IGVFFI1689RHYO/), [IGVFFI1536UVHE](/sequence-files/IGVFFI1536UVHE/), [IGVFFI5897BWCM](/sequence-files/IGVFFI5897BWCM/), [IGVFFI8523MTTA](/sequence-files/IGVFFI8523MTTA/), [IGVFFI4625YLHF](/sequence-files/IGVFFI4625YLHF/), [IGVFFI6931DXDX](/sequence-files/IGVFFI6931DXDX/), [IGVFFI6351WFDB](/sequence-files/IGVFFI6351WFDB/), [IGVFFI6583HJIU](/sequence-files/IGVFFI6583HJIU/), [IGVFFI0940IOIJ](/sequence-files/IGVFFI0940IOIJ/), [IGVFFI7401WDHX](/sequence-files/IGVFFI7401WDHX/), [IGVFFI8637NOPF](/sequence-files/IGVFFI8637NOPF/), [IGVFFI9994CUGY](/sequence-files/IGVFFI9994CUGY/), [IGVFFI9755GBJL](/sequence-files/IGVFFI9755GBJL/), [IGVFFI4103EQTP](/sequence-files/IGVFFI4103EQTP/), [IGVFFI6198EAWR](/sequence-files/IGVFFI6198EAWR/), [IGVFFI5540WROU](/sequence-files/IGVFFI5540WROU/), [IGVFFI5055ZMNZ](/sequence-files/IGVFFI5055ZMNZ/), [IGVFFI5322XBWP](/sequence-files/IGVFFI5322XBWP/), [IGVFFI6732TVQY](/sequence-files/IGVFFI6732TVQY/), [IGVFFI6818BANT](/sequence-files/IGVFFI6818BANT/), [IGVFFI1319JZCW](/sequence-files/IGVFFI1319JZCW/), [IGVFFI1985KMKT](/sequence-files/IGVFFI1985KMKT/), [IGVFFI9888EFWU](/sequence-files/IGVFFI9888EFWU/), [IGVFFI3455PHDZ](/sequence-files/IGVFFI3455PHDZ/), [IGVFFI3073VMAZ](/sequence-files/IGVFFI3073VMAZ/), [IGVFFI9794EHWW](/sequence-files/IGVFFI9794EHWW/), [IGVFFI0144HLFG](/sequence-files/IGVFFI0144HLFG/), [IGVFFI5918WWIR](/sequence-files/IGVFFI5918WWIR/) 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/IGVFDS9127RZLI/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9127RZLI](/measurement-sets/IGVFDS9127RZLI/) has sequence file(s): [IGVFFI5174DBSG](/sequence-files/IGVFFI5174DBSG/), [IGVFFI6843MNDS](/sequence-files/IGVFFI6843MNDS/), [IGVFFI3922VCPP](/sequence-files/IGVFFI3922VCPP/), [IGVFFI4085QSPN](/sequence-files/IGVFFI4085QSPN/), [IGVFFI1423UTDZ](/sequence-files/IGVFFI1423UTDZ/), [IGVFFI0799ZPYK](/sequence-files/IGVFFI0799ZPYK/), [IGVFFI3487CNKY](/sequence-files/IGVFFI3487CNKY/), [IGVFFI3485NRKR](/sequence-files/IGVFFI3485NRKR/), [IGVFFI8197IMOS](/sequence-files/IGVFFI8197IMOS/), [IGVFFI3339JEGG](/sequence-files/IGVFFI3339JEGG/), [IGVFFI4948ONLC](/sequence-files/IGVFFI4948ONLC/), [IGVFFI5434NZLG](/sequence-files/IGVFFI5434NZLG/), [IGVFFI8147DKKP](/sequence-files/IGVFFI8147DKKP/), [IGVFFI1776BCXZ](/sequence-files/IGVFFI1776BCXZ/), [IGVFFI7884POCN](/sequence-files/IGVFFI7884POCN/), [IGVFFI0281YRYH](/sequence-files/IGVFFI0281YRYH/), [IGVFFI1446TUPZ](/sequence-files/IGVFFI1446TUPZ/), [IGVFFI8373MHJM](/sequence-files/IGVFFI8373MHJM/), [IGVFFI2924KQZD](/sequence-files/IGVFFI2924KQZD/), [IGVFFI3319ZLNA](/sequence-files/IGVFFI3319ZLNA/), [IGVFFI1689RHYO](/sequence-files/IGVFFI1689RHYO/), [IGVFFI1536UVHE](/sequence-files/IGVFFI1536UVHE/), [IGVFFI5897BWCM](/sequence-files/IGVFFI5897BWCM/), [IGVFFI8523MTTA](/sequence-files/IGVFFI8523MTTA/), [IGVFFI4625YLHF](/sequence-files/IGVFFI4625YLHF/), [IGVFFI6931DXDX](/sequence-files/IGVFFI6931DXDX/), [IGVFFI6351WFDB](/sequence-files/IGVFFI6351WFDB/), [IGVFFI6583HJIU](/sequence-files/IGVFFI6583HJIU/), [IGVFFI0940IOIJ](/sequence-files/IGVFFI0940IOIJ/), [IGVFFI7401WDHX](/sequence-files/IGVFFI7401WDHX/), [IGVFFI8637NOPF](/sequence-files/IGVFFI8637NOPF/), [IGVFFI9994CUGY](/sequence-files/IGVFFI9994CUGY/), [IGVFFI9755GBJL](/sequence-files/IGVFFI9755GBJL/), [IGVFFI4103EQTP](/sequence-files/IGVFFI4103EQTP/), [IGVFFI6198EAWR](/sequence-files/IGVFFI6198EAWR/), [IGVFFI5540WROU](/sequence-files/IGVFFI5540WROU/), [IGVFFI5055ZMNZ](/sequence-files/IGVFFI5055ZMNZ/), [IGVFFI5322XBWP](/sequence-files/IGVFFI5322XBWP/), [IGVFFI6732TVQY](/sequence-files/IGVFFI6732TVQY/), [IGVFFI6818BANT](/sequence-files/IGVFFI6818BANT/), [IGVFFI1319JZCW](/sequence-files/IGVFFI1319JZCW/), [IGVFFI1985KMKT](/sequence-files/IGVFFI1985KMKT/), [IGVFFI9888EFWU](/sequence-files/IGVFFI9888EFWU/), [IGVFFI3455PHDZ](/sequence-files/IGVFFI3455PHDZ/), [IGVFFI3073VMAZ](/sequence-files/IGVFFI3073VMAZ/), [IGVFFI9794EHWW](/sequence-files/IGVFFI9794EHWW/), [IGVFFI0144HLFG](/sequence-files/IGVFFI0144HLFG/), [IGVFFI5918WWIR](/sequence-files/IGVFFI5918WWIR/) 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/IGVFDS9127RZLI/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9127RZLI](/measurement-sets/IGVFDS9127RZLI/) 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/IGVFDS9127RZLI/"
}
]
},
"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": "2024-11-25T23:52:13.786180+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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"aliases": [
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},
{
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},
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},
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},
{
"@id": "/sequence-files/IGVFFI4948ONLC/",
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],
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"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": "2024-11-26T06:10:19.621582+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": "6f24623c-fd4c-450c-b958-0d0172d678b1"
}