Monthly Archives:: July 2015

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 »

No code required

Posted by & filed under Ostrea lurida.

Today Sam and I took care of the daily maintenance of F2 Olympia oysters grown at the Ken Chew Shellfish Hatchery at Manchester, WA. In short, larvae are being described from Fidalgo (North: NF), Oyster Bay (South: SS), and Hood Canal (HC) broodstock. Though I had done most aspects before, never without Katherine, thus she… Read more »

Second look at Geoduck transcriptome

Posted by & filed under Panopea generosa.

Last week I popped out a quick assembly and annotation on our geoduck gonadal transcriptome. A second assembly was also done using Trinity. Updates August 3 – Confirmed // in file location had no impact on assembly. July 14 – TransDecoder protein annotations 10:40am – added TransDecoder results 10:29am – added Stats via Trinity Output… Read more »

There is something about TEs

Posted by & filed under Cgigas DNA Methylation.

For purposes of proposaling and reports, I have gone back to look at a small project done in collaboration with scientist at IFREMER looking at pesticide exposure on oyster larvae methylation. The control library had limited yield so the number of loci with data from the treated and the control library was restricted. However using… Read more »

Heat Stress DDMRs

Posted by & filed under Cgigas DNA Methylation.

Here is a summary of 10 Dramatically Differentially Methylated Regions (DDMRs), that is, those covered in this post that are found across a majority of the oysters exposed to acute heat shock. —

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 »