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RNA editing using the flap endonuclease 1 guided by hairpin DNA probes

GSE152883 Homo sapiens Expression profiling by high throughput sequencing 4 samples Submitted 2023/06/20 Platform GPL24676
Summary
Here we characterized a flap endonuclease 1 (FEN1) plus hairpin DNA probe (hpDNA) system, called the HpSGN system, for both DNA and RNA editing without sequence limitation.To investigate the mRNA on/off target cleavage effective of the HpSGN system,we co-transformed HepG2 (liver hepatocellular cells) with plasmids encoding FEN1 with NES and two groups of hpDNAs targeting the mRNA of AFP (Alpha Fetoprotein) gene and CDK9 (Cyclin-dependent kinase 9) gene, respectively. RNA-seq was used to examine the on/off taget cleavage effective.We proved the HpSGN system can knock down specific mRNAs in human cells at a level of ~25%.At the same time,it indicated that a degree of off-targets occur in HpSGN-treated cells.
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Direct links to NCBI, no account and no request form: the whole study as GSE152883_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 4 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA640759 and SRA study SRP268133. Searching any of these in the dataset finder brings you back here.

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