Journal: Frontiers in Genetics

Article Title: FeatSNP: An Interactive Database for Brain-Specific Epigenetic Annotation of Human SNPs

doi: 10.3389/fgene.2019.00262

Figure Lengend Snippet: Epigenetic annotation and eQTL information of SNP rs8070723 tagged genomic loci retrieved from FeatSNP. (A) Clustering visualization of epigenetic annotation to the genomic loci tagged by SNP rs8070723. (B) WashU EpiGenome Brower view of genomic loci tagged by rs8070723. Top: DNA methylation level of CpG sites in four neuronal cells. Middle track: Epilogos visualization of chromHMM predicted chromatin status. Followed eQTL tracks: log10 transformed p -value of eQTL in 10 brain regions. TAD track: Topological Associated Domain tracks of GM12878, IMR90, and Hap1. Bottom: RefSeq gene annotation track. (C) Complete eQTL information of SNP rs8070723 in 10 brain regions.

Article Snippet: The browser also displays DNA methylation data (Whole Genome Bisulfite Sequencing) of 4 neuronal progenitor and brain tissues generated by Roadmap Epigenomics Project, enhanced epilogos visualization of all 127 epigenomes, and topologically associating domains (TAD) data of GM12878, IMR90, and Hap1 cell lines ( ; ). eQTL data of 10 brain tissues generated by GTEx consortium were also visualized on the embedded WashU epigenome browser.

Techniques: DNA Methylation Assay, Transformation Assay

Journal: Genome Research

Article Title: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing

doi: 10.1101/gr.279159.124

Figure Lengend Snippet: Overall comparison of DNA methylation calls between R9 and R10 data sets across the HG002 cell line, blood, and brain samples. ( A ) Methylation proportions of R9 (orange) and R10 (blue) data for the HG002 cell line when binned by bisulfite (green) methylation intervals. The portions of R9 and R10 methylation distributions that agree with the bisulfite methylation range are highlighted in green. ( B–D ) The violin plots underneath show methylation proportions of R9 and R10 data for the HG002 cell line, brain sample, and blood sample binned according to R9 intervals. Each violin plot has lines connecting the median interval points for better visualization of methylation trends. Distributions of CpG site methylation frequencies are depicted on the right side of each panel. ( E ) Stacked bar charts showing the breakdown of total CpG sites per technology per sample. These sites are further subset into CpG sites with 0% methylation frequency and 100% methylation frequency .

Article Snippet: The HG002 EpiQC bisulfite sequencing MethylSeq data set used to benchmark the HG002 ONT bisulfite sequencing data set was generated as part of the SEQC2 Epigenomics Quality Control Study ( ).

Techniques: Comparison, DNA Methylation Assay, Methylation

Journal: Genome Research

Article Title: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing

doi: 10.1101/gr.279159.124

Figure Lengend Snippet: Genome-wide and regional methylation calling trends in HG002 R9 and R10 data sets. ( A ) Methylation calls for all CpG motifs (strand combined) in HG002 R9 and R10. ( B ) Scatterplot of 2 kb whole-genome windows with a minimum of 10 CpGs for R9 and R10. The 0–100 diagonal line is overlaid in cyan for reference. ( C , D ) Average methylation over the 29,124 filtered human promoters with a minimum of 10 CpGs plotted as a histogram and a scatter plot. ( E,F ) A histogram and scatter plot of the CpG island BED regions with more than 10 CpGs in HG002. All plots are limited to CpG sites with >5× read coverage. The y -axis is log scaled.

Article Snippet: The HG002 EpiQC bisulfite sequencing MethylSeq data set used to benchmark the HG002 ONT bisulfite sequencing data set was generated as part of the SEQC2 Epigenomics Quality Control Study ( ).

Techniques: Genome Wide, Methylation

Journal: Genome Research

Article Title: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing

doi: 10.1101/gr.279159.124

Figure Lengend Snippet: Comparison of HG002 immortalized cell line methylation calling between technologies. ( A ) Methylation proportion histograms for each technology. ( B ) Pairwise site-specific CpG methylation proportion comparison between technologies. ( C ) Site-specific CpG methylation proportion comparison between R10 and bisulfite sequencing. ( D ) RMSE values for pairwise comparisons between technology in Illumina 150 bp paired-end mappable regions as defined by BisMap. ( E ) RMSE for pairwise comparisons between technologies in Illumina 150 bp paired-end hard-to-map regions.

Article Snippet: The HG002 EpiQC bisulfite sequencing MethylSeq data set used to benchmark the HG002 ONT bisulfite sequencing data set was generated as part of the SEQC2 Epigenomics Quality Control Study ( ).

Techniques: Comparison, Methylation, CpG Methylation Assay, Methylation Sequencing

Journal: Genome Research

Article Title: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing

doi: 10.1101/gr.279159.124

Figure Lengend Snippet: Haplotype-specific methylation differences and similarities between cell, blood, and brain samples. From top to bottom , each plot shows the genome coordinates, labeled gene models (if present), haplotype-aware read mappings with modified bases as black (methylated), or colored (unmethylated) circles, a smoothed methylation fraction plot, and a coverage plot. The highlighted region corresponds to a 75 bp deletion (Chr16:88,534,247–88,534,321) in haplotype 2 of the HG002 cell line that coincides with haplotype-specific methylation. Coordinates across the bottom refer to methylation bins used in the smoothed methylation plot. ( A ) Haplotype-specific methylation differences and similarities between the R9 and R10 sequenced HG002 cell line. ( B ) Haplotype-specific methylation differences and similarities between the R10 sequenced cell line, blood, and brain samples.

Article Snippet: The HG002 EpiQC bisulfite sequencing MethylSeq data set used to benchmark the HG002 ONT bisulfite sequencing data set was generated as part of the SEQC2 Epigenomics Quality Control Study ( ).

Techniques: Methylation, Labeling, Modification