Extended Data Fig. 2: The recurrent peaks identified by MeRIP-seq/m6A-seq.
From: Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library
Three commercial antibodies (NEB [E1610S], SYSY [202003] and Abcam [ab190886]) and two popular peak calling algorithms (Macs2 and exomePeak2) are applied for peak identification (see Supplementary Methods section 2 for detailed description). (a-c) The overlapping peaks identified by MeRIP-seq/m6A-seq using different antibodies. Cellular mRNA and corresponding IVT RNA are derived from HEK293T cells. d) Ratio of recurrent peaks in published MeRIP-seq datasets for human (n = 143) and mouse (n = 66). The m6A-irrelevant peaks (IVT peaks) are compared to specific datasets derived from HEK293T (n = 10) or mESCs (n = 14). Box boundaries represent 25th and 75th percentiles; the center line represents the median; whiskers indicate ±1.5× interquartile range (IQR). The same definition for box plot is also applied for panel (h). e) Cumulative frequency curves of IVT peaks recurrently identified in published datasets using different antibodies and peak calling software. f) Representative gene loci showing the false positive peaks identified in published datasets. The accumulated reads with dark colors represent the peaks in IP samples, whereas the light colors represent the reads from input samples. g) Venn diagram showing the miCLIP peaks in cellular mRNA and IVT RNA library. h) Ratio and counts of m6A-irrelevant peaks identified by miCLIP which recurrently appear in published MeRIP-seq datasets (n = 143). The datasets derived from HEK293T (n = 10) are separately processed and compared. m6A-irrelevant peaks identified by MeRIP-seq in this study are also processed and illustrated for comparison. Detailed information of published datasets used in this study is provided in Supplementary Table 6.
