Just created a blurb for our RRBS applications! If you are limited with initial amount of DNA and/or sequencing budget, this would be a way to go! Details on the cost will be updated in a few months!
As Director of Penn State Hershey Genome Sciences Facility (http://www.pennstatehershey.org/web/core/gene-expression-analysis-overview, http://sites.psu.edu/yuka/sample-page/), my mission is to support “from start to end” genomic research. I believe our core is one of a few that can include/conduct fast and comprehensive bioinformatics analyses at competitive cost. To keep up with the fast-paced and constantly evolving NGS methodologies, we thrive to install new instruments, develop new methods and increase our computational power. One of the cutting-edge technologies we have recently developed and currently in preparation of its manuscript is a genome-wide Reduced Representation Bisulfite Sequencing (RRBS), a robust and cost effective alternative to conventional Methyl-seq technology to determine DNA methylation throughout the genome. This method generates a specific, reduced representation of the genome of DNA fragments enriched for CpG dinucleotides. Our method requires only 5 ng DNA as an input, which is about 10 times less than what other genomics core or commercially available kits do, and is thus well suited for characterizing precious samples. The development of this higher-throughput genome-wide methylation analysis has allowed Penn State Hershey’s multiple investigators’ successful achievement of DNA methylation analysis as shown in below references. Given that all of my staff has been well trained for executing “from start to end” RRBS workflows, that typically involve DNA extraction, quality control, followed by library preparation, HiSeq operation and bioinformatics analyses, I am confident we are a one-of-a-kind powerful genomics core that can conduct from soup to nut genomics projects to meet each investigator’s needs.
- Sun, Y., El-Bayoumy, K., Imamura, Y., Salzberg, A., Aliaga, C., Gowdahalli, K., Amin, S., Chen, K. Genome-wide analysis of DNA methylation induced by environmental carcinogen dibenzo[def,p]chrysene in ovarian tissues of mice. American Association for Cancer Research, (2016).
- Sun, Y., Chen, K., Imamura Kawasawa, Salzberg, A., Aliaga, C., Gowdahalli, K., Amin, S., Stoner, G., El-Bayoumy, K. The effects of the environmental carcinogen dibenzo[a,l]pyrene on genome-wide methylation and the impact of dietary black raspberry in mouse oral tissues. Cancer Research75 (15 Supplement), 2955-2955 (2015).
- Berg, A., Imamura Kawasawa, Y., Salzberg, A., Bixler, E.O., He, F., Liao, D. Abstract P260: Obesity is associated with DNA Methylation in Population-Based Adolescents. Circulation 131 (Suppl 1), AP260-AP260 (2015).