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SRX4135974: GSM3163043: 4B2N1-C1; Mus musculus; OTHER
1 ILLUMINA (Illumina NovaSeq 6000) run: 48.4M spots, 14.5G bases, 4.4Gb downloads

Submitted by: NCBI (GEO)
Study: Whole exome sequencing analyzed the off-target effect of gene editing through BE3 system.
show Abstracthide Abstract
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.
Sample: 4B2N1-C1
SAMN09274978 • SRS3349919 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina NovaSeq 6000
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: Mouse genomic DNA of cells and mice was isolated using the TIANamp Genomic DNA Kit (TIANGEN) Firstly, the genomic DNA randomly break into 150~300 bp by ultrasonic apparatus and purified with magnetic beads. Then, the product requires end repair, A-tailing, adapter ligation. The ligated products need to purify with magnetic beads again and obtain library through PCR amplification. The library was captured by Agilent Sure Select Mouse All Exon Kit and purified, amplified. The quality of sequencing library tested by Qubit and Agilent 2100 Bioanalyzer.
Experiment attributes:
GEO Accession: GSM3163043
Links:
Runs: 1 run, 48.4M spots, 14.5G bases, 4.4Gb
Run# of Spots# of BasesSizePublished
SRR722956148,378,08814.5G4.4Gb2018-08-07

ID:
5621874

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