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Series GSE115017 Query DataSets for GSE115017
Status Public on Aug 06, 2018
Title Whole exome sequencing analyzed the off-target effect of gene editing through BE3 system.
Organism Mus musculus
Experiment type Genome variation profiling by high throughput sequencing
Summary We used the whole exome sequencing to analyze the off-target effect of base editing system in mouse genomic DNA, which was extracted from haploid stem cells, mouse tails of semi-cloned embryos and mutant pups. The purpose of this sequencing is to find whether there exists off-target effect in the genome. By obtaining over 100 million reads of each sample from WES, we mapped the reads to the reference data base (mm10) and calculated the numbers of SNVs and indels. After filtering out naturally-occurring variants in the SNP database (dbSNP) and excluding SNPs also found in the wild-type genome, we next compared the DNA sequences at the remaining SNP sites with the on-target sequence. The results indicated that rare off-targets events happened in tested cell and embryos.
Overall design The off-target effect of 5 different sgRNAs in 11 different edited cell and tissue samples and 3 control samples.
Contributor(s) Jinsong L, Qing L
Citation(s) 30275529
Submission date May 29, 2018
Last update date Mar 08, 2019
Contact name Qing Li
Organization name Chinese Academy of Science
Department institute of biochemistry and cell biology
Lab Jinsong Li's Lab
Street address 320 Yueyang Road
City Shanghai
ZIP/Postal code 200031
Country China
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (14)
GSM3163042 4B2N1-C
GSM3163043 4B2N1-C1
GSM3163044 4B2N1-C2
BioProject PRJNA473524
SRA SRP149179

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
GSE115017_RAW.tar 59.5 Mb (http)(custom) TAR (of VCF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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