DNA Methylation

The Genomics Shared Resource provides DNA methylation services for both genome-wide as well as targeted studies. For genome-wide methylation analysis the GSR utilizes Infinium MethylationEPIC BeadChip as well as NGS based TruSeq DNA Methylation- whole genome bisulfite sequencing, and TruSeq Methyl Capture sequencing.

Illumina

Genome-wide methylation analysis using Illumina's Infinium MethylationEPIC BeadChip requires samples to be run in batches of 16. We require 1ug of high molecular weight DNA (via picogreen quantitation) per sample.

Illumina's MethylationEpic BeadChip contains >850K of highly informative CpG sites covering 99% of RefSeq genes, and 95% of all known CpG islands, along with enhancer sits and other content categories. The array encompasses CpG sites outside of CpG islands, Non-CpG methylated sites, differentially methylated sites identified in tumor versus normal, FANTOM 5 enhancers, ENCODE open chromatin and enhancers, miRNA promoters and DNase hypersensitive sites. The MethylationEpic array contains over 90% of the CpGs on the Illumina Methylatio450 plus an additional 350,000 CpGs in enhancer regions.

Whole Genome Bisulfite Sequencing

The TruSeq DNA Methylation Kit converts bisulfite-treated, ssDNA into an Illumina sequencing library. Only 50ng of DNA is required to create a TruSeq DNA Methylation Kit library. All ssDNA fragments are captured during the procedure, elminiating sample loss associated with other methods. WGBS-Seq covers all genes and > 38M CpGs in humans.

TruSeq Methyl Capture

The TruSeq Methyl Capture EPIC Library prep kit, which spans the full human methylome and contains over 3 million CpG sites, prepares targeted Methyl-Seq libraries for NGS. Targeted Methyl-Seq is a cost-effective method for large scale screening studies and can support both screening and biomarker discovery study objectives. As well as covering traditional epigenetic regions, TruSeq Methyl Capture EPIC offers higher coverage of emerging epigenetic regions of interest as well as siginicant coverage of CHG (H stands for A, T or C nucleotides) and CHH sites.

Core Grant Citation

This shared resource is funded by NCI P30CA16056. Publications should cite the Core grant in the acknowledgment section, if publications use data generated by the shared resource. Two copies of the publication acknowledging the Core grant should also be submitted to the facility at Elm & Carlton Streets, Buffalo, NY 14263.