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Series GSE232151 Query DataSets for GSE232151
Status Public on May 31, 2024
Title Massively parallel saturation genome editing of an essential mitochondrial targeting sequence (Tn5)
Organism Homo sapiens
Experiment type Other
Summary We employed saturation genome editing (SGE) to assess the functional consequences of synonymous, missense, and nonsense variants across KARS1 exon 2. Deep DNA sequencing of fixed-amplicon PCR products targeting the endogenous KARS1 Exon 2 locus was used to determine variant frequencies as part of a larger study to identify a set of reproducible enrichment scores indicating effects of variants on KARS1 function.
 
Overall design Tagmented libraries were prepared for homology-directed repair template pDNA and genomic DNA collected from HAP1 cells (4 biological replicates for two different sgRNAs) transfected with sgRNA only or sgRNA + HDR template at two passages post-puromycin selection (p1, p2) to assess overall sgRNA efficacy and HDR knock-in rates for saturation genome editing.
 
Contributor(s) Antonellis A, Forrest M
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Submission date May 10, 2023
Last update date May 31, 2024
Contact name Anthony Antonellis
E-mail(s) antonell@umich.edu
Organization name University of Michigan
Department Human Genetics
Lab Antonellis
Street address 1241 Catherine St
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (21)
GSM7316512 HDR template library pDNA Tn5
GSM7316513 HAP1 sgRNA1 + GFP control passage 1 Tn5
GSM7316514 HAP1 sgRNA1 + GFP control passage 2 Tn5
This SubSeries is part of SuperSeries:
GSE232152 Massively parallel saturation genome editing of an essential mitochondrial targeting sequence
Relations
BioProject PRJNA971138

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE232151_RAW.tar 3.7 Mb (http)(custom) TAR (of BAM, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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