GSE176352
RNA methylation in diabetes [RNA-Seq]
N6-methyladenosine (m6A) is one of the most prevalent and abundant epigenetic modifications in various fundamental bioprocesses. We hypothesized that m6A-mediated inflammation pathway contributes to diabetes. Total RNA was extracted from the retinas of wide type rat and their littermates with diabetes by STZ injection. A total amount of 1 µg RNA per sample was used as an input for the RNA sample preparations. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia), the reagents used in library preparation are NEBNext® Ultra RNA Library Prep Kit for Illumina (NEB, USA) .After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. The MeRIP-seq was carried out in Novogene (Beijing, China). Briefly, 2 µg total RNA was extracted from the retinas of both wide type mice and their littermates with diabetes. The integrity and concentration of extracted RNA was detected using an Agilent 2100 bioanalyzer (Agilent) and simpliNano spectrophotometer (GE Healthcare), respectively. Fragmented RNA (~100 nt) was incubated for 2 hours at 4 ? with anti-m6A polyclonal antibody (Synaptic Systems) in the immunoprecipitation experiment. Then, immunoprecipitated RNA or input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols. The sequencing was carried out with three independent biological replicates. Overall design: Differentially expressed mRNA and m6A peaks were explored by RNA-seq combined with MeRIP-seq in triplicates using Illumina novaseq 6000