Tracks display single CpG-site resolution genome-wide DNA methylation maps generated by whole genome shotgun bisulfite sequencing (WGBS). Each track displays data derived from one tissue type of one or several individual(s).
DNA methylation in the human genome mainly occurs at cytosine bases in the CpG dinucleotide context. Promoter-focussed studies established the role of DNA methylation as a stable silencing epigenetic mark (1). However, more recent findings suggest DNA methylation to be dynamic and its regulatory impact to be context dependent (2, 3).
DNA methylation mapping relied on the detection of cytosine / thymidine polymorphisms after bisulfite conversion. Treatment of genomic DNA with sodium bisulfite induces the deamination ofunmethylated cytosine bases to uracil, while methylated cytosine bases remain unchanged (4). Hence, after PCR, unmethylated cytosines are detected as thymidines whereas remaining cytosines indicate cytosine methylation. The tracks display cytosine DNA methylation as percentage of reads with a thymine versus a cytosine (0 - 100%).
Data were generated by the EMC Group at McGill based on a uniform processing pipeline. These datasets were used in all downstream analysis pipelines by members of the EMC Group at McGill.
The WGBS library preparation protocol can be found at http://ihec-epigenomes.org/outcomes/protocols/.
Genomic DNA was extracted using standard techniques.
Genomic DNA was spiked with unmethylated λ DNA and fragmented. Fragments underwent end repair, adenylation of 3'ends, and adaptor ligation. Adaptor ligated DNA was bisulfite converted followed by amplification by PCR. Library qualities were assessed using the Agilent 2100 BioAnalyzer (Agilent Technologies).
Libraries were sequenced on Illumina HiSeq2000 or HiSeq2500 systems. WGBS data processing was carried out as described by Johnson et al. (5). In short, reads were aligned to the bisulfite converted reference genome using BWA; (i) clonal reads, (ii) reads with low mapping quality score, (iii) reads with mismatches to converted reference, (iv) reads mapping on the forward and reverse strand of the bisulfite converted genome, (v) read pairs not mapped at the expected distance based on library insert size, and (vi) read pairs that mapped in the wrong direction were removed. Data have been deposited to http://epigenomesportal.ca.
Data were generated and processed in the Epigenomic Mapping Centre (EMC) and Epigenomic Data Coordination Centre (EDCC) of McGill University and the Genome Quebec Innovation Centre (Montreal,QC, Canada). Both EMC and EDCC belong to the Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) associated with IHEC. Funding was obtained from the Canadian Institutes of Health Research (CIHR) in partnership with Genome British Columbia and Genome Quebec. For inquiries, please contact us at the following address: info (at) epigenomesportal.ca