Table 1.
Overview of study design for the MethylMiner versus MethylCap comparison and number of reads in each condition.
Captured DNA (ng) indicates the amount of DNA that was captured in the MBD enrichment; % Mapped Reads are percent of the Total Reads that successfully aligned and % Used Reads are percent of the Total Reads that successfully aligned and remained after rigorous quality control.
Fig 1.
Methylation signals and levels of background noise.
The mean coverage of CpGs and non-CpGs from MethylMiner and MethylCap, respectively are shown. The horizontal lines indicate the threshold for background noise as determined by the 95th percentile of the estimated coverage of the non-CpGs for MethylMiner and MethylCap, respectively.
Fig 2.
The overlap of MethylMiner and MethylCap with local CpG density.
The local CpG density is plotted against the percentage CpG coverage. The distribution of the local CpG density in the reference sequence is the highest outside of CpG-rich regions. Better coverage of the regions where the majority of CpGs occur (in the range of 1–7 CpGs) is obtained with MethylMiner than with MethylCap.
Fig 3.
The effect of altered salt concentrations for elutions in MethylMiner.
The shown data was generated as part of our recent methylome-wide investigations in humans[5]. The local CpG density is plotted against the percentage CpG coverage for two randomly selected individuals in the upper and lower graph, respectively. As expected, the unenriched genomic DNA closely follows the distribution of the CpG density in the reference genome. Best coverage of the regions where the majority of CpGs occur (in the range of 1–7 CpGs) is obtained by a single MethylMiner elution using a low salt (0.5M NaCl) buffer. Using a single elution with a higher salt (2.0M NaCl) concentration moves the distribution to regions with higher CpG density. If performing a double elution where the low salt elution is discarded and only the 2nd fraction eluted with the high salt buffer is investigated, the distribution is shifted even further to the right excluding regions with low local CpG density and focusing mainly in regions with high CpG density.
Fig 4.
The effect of altered salt concentrations for elutions in MethylCap.
The local CpG density is plotted against and the percentage CpG coverage. The distribution of the local CpG density in the reference genome is shown. The distribution of CpG coverage for MethylCap is shown when using a low salt elution buffer and when using a high salt elution buffer.