10.6084/M9.FIGSHARE.16896287.V1
Yanan Han
Yanan
Han
Air Force Medical University
Galina Yurevna Zheleznyakova
Galina Yurevna
Zheleznyakova
Yanara Marincevic-Zuniga
Yanara
Marincevic-Zuniga
Majid Pahlevan Kakhki
Majid Pahlevan
Kakhki
Amanda Raine
Amanda
Raine
Uppsala University
Maria Needhamsen
Maria
Needhamsen
Maja Jagodic
Maja
Jagodic
Karolinska University Hospital
Comparison of EM-seq and PBAT methylome library methods for low-input DNA
<p>DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1-10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole genome methylation quantification of low input samples.</p>
Biophysics
Biochemistry
Genetics
Molecular Biology
39999 Chemical Sciences not elsewhere classified
Science Policy
69999 Biological Sciences not elsewhere classified
Inorganic Chemistry
Plant Biology
Taylor & Francis
2021
2021-10-28
2022-10-06
Journal contribution
5171625 Bytes
10.1080/15592294.2021.1997406
10.6084/m9.figshare.16896287
CC BY 4.0