Getting into DNA Methylation
I have to share some information with several new folks, and there are likely old folks that should give this a refresh… thus I am posting it here.
What to read
A good place to start in term of biology are a few reviews including
- Gavery, M., & Roberts, S. (2018). Genetics & Epigenetics in Life History and Reproduction: Oysters. In M. K. Skinner (Ed.), Encyclopedia of Reproduction. vol. 6, pp. 736–742. Academic Press: Elsevier. http://dx.doi.org/10.1016/B978-0-12-809633-8.20621-3 : pdf
- Gavery MR, Roberts SB. (2017) Epigenetic considerations in aquaculture. PeerJ 5:e4147 https://doi.org/10.7717/peerj.4147
- Mackenzie R. Gavery, Steven B. Roberts; A context dependent role for DNA methylation in bivalves, Briefings in Functional Genomics, Volume 13, Issue 3, 1 May 2014, Pages 217–222, https://doi.org/10.1093/bfgp/elt054
Some good primary papers include
- Dimond JL, Gamblewood SK, Roberts SB. (2017) Genetic and epigenetic insight into morphospecies in a reef coral Molecular Ecology. 00:1–12. doi: 10.1111/mec.14252
- Olson CE and Roberts SB. (2014). Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes Frontiers in Physiology. 5:224. doi: 10.3389/fphys.2014.0022
- Gavery MR and Roberts SB. (2013) Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc PeerJ 1:e215. doi:10.7717/peerj.215
There are a few other relevant products
- Gavery M, Delrow J, Basom R, Roberts S (2015) Influence of 17α-ethinylestradiol on DNA methylation in oysters. GitHub
- Olson CE, Roberts SB (2015) Indication of family-specific DNA methylation patterns in developing oysters. bioRxiv (preprint). doi: https://doi.org/10.1101/012831
If you are looking for an older deep dive.
Jumping into our Onboarding repo: Computing · RobertsLab/onboarding Wiki · GitHub is a good place to start.
Some examples of how we work can be seen here 9 Ways to Make Papers a Little More Open and Reproducible – Roberts Lab
And a recent review Roberts and Gavery (2018) OPPORTUNITIES IN FUNCTIONAL GENOMICS: A PRIMER ON LAB AND COMPUTATIONAL ASPECTS . Journal of Shellfish Research, Vol. 37, No. 3, 1–8, 2018. DOI: 10.2983/035.037.0300
- Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools: Vince Buffalo: 9781449367374: Amazon.com: Books
- R for Data Science
Gitting to Work
So now you have mastered Git, fluent in Bash, and are launching Jupyter notebooks on a regular basis. Here are some resources to get you going on analysis.
- From when Jupyter was still IPython GitHub - che625/olson-ms-nb
- A set of notebooks from on coral epigenetics. GitHub - jldimond/Coral-CpG: Repository associated with article “Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change”
- Some recent work in R : gavery-testdrive-Rproject/DMR-2-GeneIDs.Rmd at master · sr320/gavery-testdrive-Rproject · GitHub
- and my notebooks GitHub - sr320/nb-2018
If you want to play around with some data…
- Geoduck Genome : Genomic Resources · RobertsLab/resources Wiki · GitHub
- Lots of RRBS data (prefix
EPI: Index of /nightingales/P_generosa ;sample description · hputnam/project_juvenile_geoduck_OA · GitHub
- manuscript draft .
- Eastern Oyster Genome: Genomic Resources · RobertsLab/resources Wiki · GitHub
- Simple Oyster BS Comparison Data
Post any practical how-to questions here.