The Epigenetics Shared Resource provides DNA methylation analysis and epigenetics-related bioinformatics services. The experienced staff is available for help with project design and, where necessary, outsourcing for large-scale projects. Researchers are encouraged to initiate discussions regarding their project plans with the Director and Manager to best facilitate proper DNA sample preparation, targeted genomic region details, and the pipeline for data generation. Services offered are:

1. Illumina “800k” MethylationEPIC BeadChip Assay for genome-wide analysis of CpG methylation

With the MethylationEPIC BeadChip array-based analysis, researchers can interrogate over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution. This technology is ideal for cancer versus normal comparisons, and for epigenome-wide association studies (EWAS). The service includes:

  • gDNA quantification and quality control
  • MethylationEPIC BeadChip analysis
  • Return of raw data files

Statistical analysis and mapping of the resulting data to ENCODE tracks is not included in the basic service but may be requested as an additional service (see #3 below).

2. High throughput targeted methylation analysis using Fluidigm Access Array – Illumina MiSEQ

This service utilizes bisulfite treatment of genomic DNA followed by targeted sequencing for methylation analysis. The technology currently in place employs the Fluidigm Access Array system and amplicon tagging for the enrichment of targeted sequences. Libraries prepared by this method are subjected to Next Generation Sequencing (NGS) on the Illumina MiSEQ platform, which scores both net methylation in each amplicon, and yields complete information on methylation patterns, beyond that obtained from the MethylationEPIC assays. When polymorphic loci are included among the amplicons, allele-specific methylation can be queried, which can be a useful adjunct for EWAS. The complete service includes:

  • gDNA quantification and quality control
  • Bisulfite conversion
  • Primer design and synthesis
  • Library prep and quality control
  • MiSEQ sequencing and FASTQ generation
  • MiSEQ data processing: alignment to ENCODE chromatin and transcription factor tracks to produce useful mapping figures suitable for publication; methylation heatmaps by sample and amplicon; BedGraphs that allow additional analyses of data aligned to the UCSC Genome Browser

A single project consists of 48 samples x 48 amplicons or 96 samples x 48 amplicons. Before using the service, read the Sample Submission Instructions. Please note that DNA should not be dropped off unless previously arranged with the facility.

3. Custom mapping of epigenetic data from NCBI/GEO and related outside sources

The staff of the Epigenetics SR will produce custom maps of available DNA methylation datasets from outside sources, including prior publications, prior investigator-generated datasets, and public data at NCBI/GEO. Methylation heatmaps and Principle Component Analysis (PCA) can be done, and data can be aligned to ENCODE chromatin and transcription factor binding site tracks to produce useful figures. The researcher will then be provided with complete files and reports.

In addition to the above services, whole genome bisulfite sequencing on HiSeq is also available, via advice and referral to the HICCC Genomics SR and other facilities with which we have a relationship. The Epigenetics SR also provides technical assistance on custom design of research projects.