Abstract
The REPIC (RNA EPItranscriptome Collection) database records about 10 million peaks called from publicly available m6A-seq and MeRIP-seq data using our unified pipeline. These data were collected from 672 samples of 49 studies, covering 61 cell lines or tissues in 11 organisms. REPIC allows users to query N6-methyladenosine (m6A) modification sites by specific cell lines or tissue types. In addition, it integrates m6A/MeRIP-seq data with 1418 histone ChIP-seq and 118 DNase-seq data tracks from the ENCODE project in a modern genome browser to present a comprehensive atlas of m6A methylation sites, histone modification sites, and chromatin accessibility regions. REPIC is accessible at https://repicmod.uchicago.edu/repic.
Highlights
BackgroundOver 150 chemical modifications have been identified in messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs) [1]
Over 150 chemical modifications have been identified in messenger RNAs and non-coding RNAs [1]
As ribosomal RNAs (rRNAs) could potentially interfere with messenger RNAs (mRNAs) expression quantification and peak calling, we first interrogated the rRNA content in each sample. rRNA reads comprised less than 30% of total reads in 566 samples (85.0% of the total), while 371 samples (55.7% of the total) contained a proportion of rRNA reads below 5% (Fig. 2a), suggesting that most samples were not subject to rRNA contamination
Summary
Over 150 chemical modifications have been identified in messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs) [1]. RMBase v2.0 integrates information on sites of five or more types of RNA modifications, RBP binding sites, and single nucleotide polymorphisms, whereas MeT-DB v2.0 and CVm6A publish m6A peaks processed by their own pipelines from raw m6A sequencing data (Table 1). After merging different runs in the same experiment and excluding unpaired input-IP samples, 672 samples—which consisted of 339 pairs of input-IP data from 49 studies, covering 61 cell lines or tissue types in 11 organisms—were used for database construction (Additional file 1: Table S1). HOMER v4.9 [51] was used for motif enrichment analysis based on the top 2000 peaks ranked by their fold enrichment levels
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