|
|
| Home | Browser | Tools | Log Out |
Help
|
Genboree Home |
Methylation Platform Comparison
Supplementary data for the article "Sequence-based profiling of DNA methylation: comparisons of methods and catalogue of allelic epigenetic modifications".
ABSTRACT
DNA methylation profiling methods utilizing massively parallel sequencing are comprehensive, and as accuracy and affordability improves, will increasingly supplant microarrays for genome-scale methylation analyses. Here we compare four sequencing-based methodologies for genome-scale methylation assessment. We evaluate critical factors including methylome coverage, resolution, quantitative accuracy, methylation call concordance, and their relationships with CpG density and genomic context. For regions with sufficient sequence coverage, methylation calls reached 99% concordance between two bisulfite methods and between two enrichment methods and 95.5% concordance among all four methods. These in-depth comparisons and browsable datasets are a valuable resource for the increasing number of researchers investigating methylation. To achieve comprehensive methylome coverage while reducing cost, an integrative approach involving two complementary methods is examined. The integrative methylome profile along with histone methylation, RNA, and SNP profiles allowed genome-wide assessment of allele-specific epigenomic states, including most known imprinted loci and many new loci exhibiting monoallelic epigenetic states.
Interactive Browser Views of article figures
Figure 4b. Genome browser view of the Protocadherin Alpha Cluster (PCDHA) illustrating significant concordance in methylation calls across this 100kb CpG rich region.
Figure 5c. Genome Browser view of ZNF331 in H1 ES cells, showing overlap of MeDIP-seq, MRE-seq and H3K4me3 (from ChIP-seq) signals at bisulfite region 1 and MeDIP-seq only signal at bisulfite region 2.
Figure 6b. Genome Browser view of GRB10 MeDIP-seq and MRE-seq signals in human H1 ES cells showing bisulfite regions analyzed.
Figure 6c. Browser view of the methylation status of the POTEB 5' region, and indicating positions for bisulfite validation.
Supplementary Figure 6. NAP1L5 Browser View. One of the 19 known DMRs in the imprinted NAP1L5 gene is not within a CGI. The DNA methylation pattern, showing signal in both MeDIP-seq and MRE-seq, is consistent with imprinting.
Search by gene or other landmark to see H1 Methylation data
DNA methylation profiling methods utilizing massively parallel sequencing are comprehensive, and as accuracy and affordability improves, will increasingly supplant microarrays for genome-scale methylation analyses. Here we compare four sequencing-based methodologies for genome-scale methylation assessment. We evaluate critical factors including methylome coverage, resolution, quantitative accuracy, methylation call concordance, and their relationships with CpG density and genomic context. For regions with sufficient sequence coverage, methylation calls reached 99% concordance between two bisulfite methods and between two enrichment methods and 95.5% concordance among all four methods. These in-depth comparisons and browsable datasets are a valuable resource for the increasing number of researchers investigating methylation. To achieve comprehensive methylome coverage while reducing cost, an integrative approach involving two complementary methods is examined. The integrative methylome profile along with histone methylation, RNA, and SNP profiles allowed genome-wide assessment of allele-specific epigenomic states, including most known imprinted loci and many new loci exhibiting monoallelic epigenetic states.
Interactive Browser Views of article figures
Figure 4b. Genome browser view of the Protocadherin Alpha Cluster (PCDHA) illustrating significant concordance in methylation calls across this 100kb CpG rich region.
Figure 5c. Genome Browser view of ZNF331 in H1 ES cells, showing overlap of MeDIP-seq, MRE-seq and H3K4me3 (from ChIP-seq) signals at bisulfite region 1 and MeDIP-seq only signal at bisulfite region 2.
Figure 6b. Genome Browser view of GRB10 MeDIP-seq and MRE-seq signals in human H1 ES cells showing bisulfite regions analyzed.
Figure 6c. Browser view of the methylation status of the POTEB 5' region, and indicating positions for bisulfite validation.
Supplementary Figure 6. NAP1L5 Browser View. One of the 19 known DMRs in the imprinted NAP1L5 gene is not within a CGI. The DNA methylation pattern, showing signal in both MeDIP-seq and MRE-seq, is consistent with imprinting.
Search by gene or other landmark to see H1 Methylation data
|
© 2001-2024 Baylor College of Medicine
Bioinformatics Research Laboratory (400D Jewish Wing, MS:BCM225, 1 Baylor Plaza, Houston, TX 77030) |