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Global analysis of m6A mRNA methylation in human cells

ABSTRACT: m6A RNA immunoprecipitation was performed according to published procedure (Dominissini et al., 2012). Human m6A-seq data from DTSC2 HeLa cells were aligned to the hg19 transcriptome. To locate m6A peaks, the hg19 transcriptome was divided into 25 nucleotide-wide tiles. The number of reads in the m6A immunoprecipitation (IP) and non-IP (control) sample was counted in each tile, and a p-value was calculated using Fisher’s exact test and adjusted for multiple testing. Tiles with significant enrichment of the m6A signal (adjust-P value < = 0.05) were merged into larger regions. Regions lesser than 100 bp were discarded, and regions over 200 bp were separated into 100 to 200 bp sub-regions; the m6A signal from rapamycin-treated cells compared to control (DMSO) was calculated for each region; and regions with at least a two-fold enrichment in all replicates were identified as m6A peaks. The distributions of m6A peaks and m6A marked genes were identified by overlapping all m6A peaks with the hg19 RefGene annotation (Meng et al., 2014).

ORGANISM(S): Homo sapiens

PROVIDER: GSE165690 | GEO | 2021/02/17

REPOSITORIES: GEO

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