Journal: Journal of Molecular Cell Biology

Article Title: MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution

doi: 10.1093/jmcb/mjv037

Figure Lengend Snippet: General information of the sequencing data for MethylC-seq, MB-seq, RRBS, and MeDIP-seq.

Article Snippet: Given the fact that NIH Roadmap Epigenomics Project's current release of the Human Epigenome Atlas deposited 108 RRBS data sets for 67 tissues or cell lines with only 5 of these samples being MethylC-seq data sets, by performing MB-seq on these samples, our new method, MBRidge could convert the data into single-CpG resolution, genome-wide methylomes, and thus significantly increase value of the existing datasets.

Techniques: Sequencing, Methylated DNA Immunoprecipitation, Methylated DNA Immunoprecipitation Sequencing, Methylation

Journal: Journal of Molecular Cell Biology

Article Title: MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution

doi: 10.1093/jmcb/mjv037

Figure Lengend Snippet: The comparison of different DNA methylation profiling methods used at single-CpG resolution. (A and B) CpG coverage as a function of read coverage threshold for MethylC-seq (cyan), RRBS (medium-orchid), and MB-seq (green). X-axis denotes sequencing depth and y-axis denotes the fraction of CpGs that are at or above a given sequencing depth. The percentage of CpGs that were covered genome-wide (A) or in repeat (B) are plotted. (C) Venn diagram shows the overlap of mCpGs from three methylation profiling methods. The total mCpGs measured by all three methods and percentages for each color block are shown. The three circles represent MethylC-seq (blue), RRBS (green), and MB-seq (red), respectively. (D) Barplot represents the fraction of mCpG covered only by MethylC-seq, but not by MB-seq or RRBS.

Article Snippet: Given the fact that NIH Roadmap Epigenomics Project's current release of the Human Epigenome Atlas deposited 108 RRBS data sets for 67 tissues or cell lines with only 5 of these samples being MethylC-seq data sets, by performing MB-seq on these samples, our new method, MBRidge could convert the data into single-CpG resolution, genome-wide methylomes, and thus significantly increase value of the existing datasets.

Techniques: Comparison, DNA Methylation Assay, Sequencing, Genome Wide, Methylation, Blocking Assay

Journal: Journal of Molecular Cell Biology

Article Title: MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution

doi: 10.1093/jmcb/mjv037

Figure Lengend Snippet: Experimental validation of DMRs between T29 and T29H cell lines identified by MBRidge. Genome browser views and line graphs show the DMRs between T29 and T29H, validated by locus-specific bisulfite sequencing. The line graph shows the methylation levels measured by MethylC-seq, RRBS, bisulfite PCR validation (BS-PCR), and MBRidge. (A) A representative DMR in chr10: 50492078–50492258. MBRidge agrees with BS-PCR and MethylC-seq. (B) A representative DMR in chr11: 14870180–14870346. MBRidge agrees with BS-PCR for both T29 and T29H, while MethylC-seq and RRBS do not detect the region that is enriched by MeDIP-seq in T29 cells.

Article Snippet: Given the fact that NIH Roadmap Epigenomics Project's current release of the Human Epigenome Atlas deposited 108 RRBS data sets for 67 tissues or cell lines with only 5 of these samples being MethylC-seq data sets, by performing MB-seq on these samples, our new method, MBRidge could convert the data into single-CpG resolution, genome-wide methylomes, and thus significantly increase value of the existing datasets.

Techniques: Biomarker Discovery, Methylation Sequencing, Methylation, Methylated DNA Immunoprecipitation