REPIC

REPIC aggregates m6A-seq and MeRIP-seq data to provide a unified database of N6-methyladenosine (m6A) peak calls for epitranscriptomic analysis.

Key Features:

• Extensive Data Collection: Approximately 10 million peaks called from m6A-seq and MeRIP-seq data derived from 672 samples across 49 studies, covering 61 cell lines or tissues in 11 organisms.
• Unified Peak-Calling Pipeline: A single, consistent pipeline was applied to m6A-seq and MeRIP-seq datasets to identify m6A peaks.
• Query Functionality: Enables querying of m6A modification sites with specificity for cell lines or tissue types.
• ENCODE Data Integration: m6A/MeRIP-seq data are integrated with 1,418 histone ChIP-seq and 118 DNase-seq tracks from the ENCODE project to support combined analyses with chromatin features.

Scientific Applications:

• Cell or Tissue Specificity Profiling: Exploration of cell- or tissue-specific patterns of m6A modification across samples and organisms.
• Chromatin Correlation Analyses: Correlation of m6A modification sites with histone modification and chromatin accessibility datasets from ENCODE.
• Regulatory Mechanism Investigation: Investigation of potential regulatory roles of m6A modifications in gene regulation and cellular function.

Methodology:

A unified pipeline was applied to m6A-seq and MeRIP-seq data to call ~10 million peaks from 672 samples, and these m6A/MeRIP-seq datasets were integrated with 1,418 histone ChIP-seq and 118 DNase-seq ENCODE tracks.