A closer look at DMRs

Posted by & filed under Cgigas DNA Methylation.

A detailed look at DMRs that hold true across oysters exposed to heat shock. Updated July 6, 2015 – added three more DMRs (at bottom of post) Going down the list, scaffold418_576986 is a feature that overlaps gene EKC36328, Bromodomain-containing protein 8. Specifically the location is in the intron between exon 18 and 19 (total… 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

Differential Methylation in the Kitchen

Posted by & filed under Cgigas DNA Methylation.

Finally re-getting around to examing our MBD-array data in the context of RNA-seq data. Briefly we have three oysters that were heat shocked with samples taken prior to, and following. An MBD-array experiment was carried out where for each oyster we have information on 50bp genome features (selected probes on the array) whether the region… Read more »