The GRCF offers genome-wide and targeted methylation analysis for your project.

We support methylation projects with PCR and Bisulfite conversion services as well.

Whole Genome Arrays

HUMAN EPIC (850K) INFINIUM METHYLATION BEADCHIP

With the Infinium MethylationEPIC BeadChip Kit, researchers can interrogate over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution. Multiple samples, including FFPE, can be analyzed in parallel to deliver high-throughput power while minimizing the cost per sample.

This chip provides a pan-enhancer and coding region view of the methylome for epigenome-wide association studies. It covers the following content areas:

  • CpG sites outside of CpG islands
  • Non-CpG methylated sites identified in human stem cells
  • Differentially methylated sites identified in tumor vs. normal
  • FANTOM5 enhancers
  • ENCODE open chromatin and enhancers
  • DNase hypersensitive sites
  • miRNA promoter regions
  • >90% of the 450K BeadChip content is retained.


A list of  all CpG sites is available for download.

Number of SamplesArray pricingArray pricing with FFPE restore
93 or less (internal customers only)$370/sample$470/sample
94 - 5000$340/sample$440/sample

MOUSE INFINIUM METHYLATION BEADCHIP

The  Illumina Infinium Mouse Methylation Beadarray features more than 275,000 markers across the methylome. This allows high-resolution epigenetic analyses of diverse murine strains, which is useful for epigenome-wide association studies, xenograft experiments, preclinical research, toxicology, embryology and other applications.

Coverage includes:

  • 28,847 transcription start sites
  • miRNAPromotor transcription start sites
  • Noncoding RNA transcription start sites
  • Enhancers
  • Imprinted loci
  • 16,000 CpG islands
  • Hypermethylated regions in cancer
  • 25,000 highly conserved human EPIC array probesStrain-specific SNP probes from 18 mouse strains


A list of all CpG sites is available for download.

Number of SamplesArray pricingArray pricing with FFPE restore
93 or less (internal customers only)$355/sample$455/sample
94 - 5000$330/sample$430/sample

Full service pricing for all Illumina arrays includes:

  • 100% and 0% methylation controls (1 of each per plate)
  • Bisulfite Conversion
  • Full data release, which includes: raw intensity data, GenomeStudio Project, Methylation Profile, Samples Table, Analysis using minfi including code used, minfi output including PLINK and README docs explaining the data in each directory


For more information on these services, please contact  Roxann Ashworth [410-614-0702].

Target Methylation Analysis

Validate your Illumina array results or investigate your favorite epigenetic regions for human and rodents.

Analysis via Pyrosequencing

Specific regions of methylation can be assayed via sequencing on the Pyromark Q48 system from Qiagen, using their advanced methylation reagents. This is  not high throughput/next generation sequencing. Bisulfite converted DNA is PCR amplified with a biotinylated primer pair. The non-biotinylated strand is sequenced in the Pyromark system. A video describing the process is available on  YouTube.

Custom Pyrosequening Assays

Custom regions can be amplified, or one of the 30,000 human and rodent predesigned kits can be ordered from Qiagen. Primers  ordered through us receive a slight discount and free shipping. Assay design assistance is available for all projects being run in our facility.

Pricing

  • Individual Tubes: $10.25 each
  • Projects with more than 500 samples run at one time with the same assay: $10.00 per sample.


For more information, contact Roxann Ashworth.

PCR & Bisulfite Conversion support available.  Scroll down for more information.

Illumina iSelect Methyl Custom Chips

The Infinium HTS iSelect Methyl Custom BeadChip allows researchers and commercial customers to create made-to-order, high-throughput assays to fit their specific needs. The flexibility and features of the Infinium HTS iSelect Methyl Custom BeadChip make it a powerful tool for a wide range of epigenetic applications.

For more information, contact us.

Ancillary Services

PCR Support

If you don’t have the lab equipment and/or the time to run your own samples, we are here for you! We provide a full range of services for your pyrosequencing projects.

Full Service: includes bisulfite conversion of DNA samples (if needed), PCR of samples, amplification confirmation of the PCR by agarose gel electrophoresis and submission for Pyrosequencing. Please contact  Alejandra Gutierrez for more information.

PCR Only Support: PCR support pricing is sample number dependent. Please inquire.

Bisulfite Conversion

 Bisulfite conversion of isolated DNA is offered using Zymo Research Corporation EZ DNA Methylation Kit or Qiagen EpiTect Bisulfite Kits.

Converted DNA is suitable for PCR, endonuclease digestion, sequencing, microarrays, and Illumina Infinium and Golden Gate Methylation Assays.

  • EpiTect Bisulfite conversion: $15/sample. (Recommended for Pyrosequencing.)
  • EZ DNA Methylation conversion pricing is sample number dependent.  (Recommended for Illumina.)


Please contact Alejandra Gutierrez for pricing and ordering.