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. 2020 Apr 28;21(1):100.
doi: 10.1186/s13059-020-02012-4.

REPIC: a database for exploring the N6-methyladenosine methylome

Shun Liu  1   2   3 , Allen Zhu  2   3   4 , Chuan He  2   3   5 , Mengjie Chen  6   7
Affiliations

REPIC: a database for exploring the N6-methyladenosine methylome

Shun Liu et al. Genome Biol. .

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.

Keywords: Database; Genome browser; Tissue specificity; m6A modification.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
a Overall design of the REPIC database. b Schema of the customized pipeline for m6A-seq or MeRIP-seq data processing
Fig. 2
Fig. 2
The quality of m6A-seq or MeRIP-seq reads mapping. Boxplots depicting the distribution of reads mapped to a rRNAs and b genomes in the input and IP samples, respectively. The y-axis in a and b represents the percentage of reads mapped to rRNAs and non-rRNA reads mapped to genomes, respectively. Both left-side panels show the whole range of the ratios and the right-side panels of a and b zoom in on the ranges of 0–5% and 75–100%, respectively
Fig. 3
Fig. 3
Evaluation of similarities of peak sets generated by three peak calling tools. Scatter plots showing the distributions of the Jaccard Index and Simpson Index from comparisons of a exomePeak versus MACS2, b MeTPeak versus MACS2, and c exomePeak versus MeTPeak across all samples. Paired-end and single-end sequencing types are represented by triangles and circles, respectively. Species are indicated by colors
Fig. 4
Fig. 4
Cell- or tissue-specific m6A modifications. a Heatmap depicting the Pearson correlation of different human cell lines and tissues of the top 2000 genes ranked by CVs of fold enrichment levels of m6A peaks at stop codon regions (± 200 bp around the stop codons). The dendrogram was constructed using complete linkage based on Euclidean distances. Each row label represents the sample information in the format of “input_IP”. bt-SNE plot displaying grouping patterns of different cell/tissue samples in a lower-dimensional space for the same data in a. Each dot represents a sample. Cell/tissue types are indicated by colors
Fig. 5
Fig. 5
Screenshots of the web interfaces of the REPIC database. a The Home page. b The Search page. c Taking the query region near gene NANOG as an example, we show a visualization of m6A peaks, histone modifications, and chromatin accessibility in the genome browser
See this image and copyright information in PMC

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