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

. 2021 Jun 19;14:28. doi: 10.1186/s13072-021-00401-y

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

© The Author(s) 2021

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

PMC Copyright notice

Fig. 5 — Cytosine retention for methylation controls, namely lambda phage (A), pUC19 (B), and mitochondrial DNA (C). Lambda phage and pUC19 are added to the genomic DNA to serve as unmethylated and methylated controls, respectively. Mitochondrial DNA is a good source of unmethylated DNA that can be used in lieu of spike-in controls. Note, PBAT only had one technical replicate, so there is no “Rep. 2” half on these violins. In addition, the mitochondrial DNA required at least three reads covering each CpG, while the spike-in controls required at least one read due to the fewer number of reads relative to the genomic DNA. This coverage requirement can result in all CpGs for a sample being 1.0, such as in Kapa Sample A in B