Targeted 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 regions can be amplified, or one of the 30,000 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. Rodent primers work on both mice and rats.

For more information, contact Roxann Ashworth [410-614-0702]

Individual Tubes
Projects of more than 500 samples
run at one time with the same assay
PCR and Bisulfite Conversion Support Service

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 Laura Kasch [410-614-3830] for more information.

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

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Whole Genome Analysis (Mouse Only)

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
  • miRNA Promotor 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 probes
  • Strain-specific SNP probes from 18 mouse strains

A list of all CpG sites is available for download.

For more information on this service, please contact Roxann Ashworth.


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 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

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