Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2020 Apr 20;10:6590. doi: 10.1038/s41598-020-63355-3

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Changes in peaks between conditions. (a) Detected m6A(m) changes in thirteen published data sets that measured m6A(m) peak changes between two conditions (Supplementary Table 4). The number of peaks detected as changed in the original published analyses are compared to the number of peaks with FDR-adjusted p-values < 0.05 in our reanalysis using DESeq2, edgeR, or QNB, and taking the union of results from these three tools with additional filters for log2 fold difference in peak and gene changes of ≥1 and peak read counts ≥10 across all replicates and conditions (“filtered”). (b) Gene coverage plots for Hspa1a in mouse embryonic fibroblasts (MEFs) and HSPA1A in human cells (HepG2 and BCL) before and after heat shock. Input coverage is shown in black and IP coverage in raspberry, with putative m6A peaks changed highlighted in yellow and marked by arrows. miCLIP coverage for an experiment in HepG2 cells is shown in orange. (c) Coverage plots for PSIP1, which was reported to have a change in 5′ UTR m6A with HIV infection by Lichinchi et al. (2016). (d) Coverage plots for SUN2, in which we detected changes in m6A with HCMV infection and dsDNA treatment suggesting a possible increase in methylation under higher interferon conditions (after 12 h of dsDNA treatment compared to untreated controls and after 6 h post-HCMV infection compared to 72 h, when interferon levels have declined). Lines in coverage plots (b-d) show the mean across all replicates for each experiment, while shading shows the standard deviation. Coding sequences are shown in grey.