Epigenetic variation of two populations grown at common site

Posted by & filed under Ostrea lurida.

In a different experiment compared to when Fidalgo siblings were outplanted at two sites, we also examined Hood Canal (HC) and Oyster Bay (SS/South Sound) grown at Clam Bay (Manchester). Descriptor. These were the oysters Katherine Silliman spawned in the summer of 2015 and represent seed Jake outplanted years ago. This was run against the… Read more »

CoGe on Fidalgo Sibs

Posted by & filed under Ostrea lurida.

As per this pipeline I will run the 8 individuals in the environmental epigenetics mini-experiment. — Once complete this is all available in the genome browser

Fidalgo offspring at two locations

Posted by & filed under Ostrea lurida.

We carried out whole genome BS-Seq on siblings outplanted out at two sites: Fidalgo Bay (home) and Oyster Bay. Four individuals from each locale were examined. A running description of the data is available @ https://github.com/RobertsLab/project-olympia.oyster-genomic/wiki/Whole-genome-BSseq-December-2015. I need to look back to a genome to analyze this. We did some PacBio sequencing a while ago…. Read more »

Alternative splicing and germline methylation

Posted by & filed under Cgigas DNA Methylation.

One of the premises related to germline methylation in oysters is that genes with limited methylation will have more alternatively spliced products. One of our most robust identification of alternatively spliced genes is from the heat shock experiment, however methylation was assessed with array to ID DMRs. In order to gauge the relationship of germline… Read more »

First steps at an aggregated view of all DNA methylation data (updated)

Posted by & filed under Cgigas DNA Methylation.

Seems like I have gotten close (see here) but do not have a canonical IGV session that has all of our DNA methylation data. The goal here is to generate such a product (and publish, so I do not lose it). All data is publicly available at http://owl.fish.washington.edu/halfshell/index.php?dir=2015-05-comgenbro see also data on Figshare Updates July… Read more »

Intersecting DMRs

Posted by & filed under Cgigas DNA Methylation.

To try to determine where the DMRs defined by three *sig.bedGraph files described here are located on genome – intersectbed was used, some steps and … Full notebook @ http://nbviewer.ipython.org/github/sr320/paper-Temp-stress/blob/authorea/ipynb/Array-feature-overlap-02.ipynb tlrs

Differentially methylated loci – repeats or TEs

Posted by & filed under Cgigas DNA Methylation.

In our original effort (bioRxiv doi:¬†http://dx.doi.org/10.1101/012831) we characterized DMLs in relationship to genomic regions, including putative transposable elements. In this case TEs were defined as tandem repeats and targets that had sequence similarity to protein sequences in other species. Transposable elements were identified using RepeatMasker, a program that screens and annotates interspersed repeats (Smit et… Read more »