Posts By: Steven Roberts

Another day, another species

Posted by & filed under Ostrea lurida.

Today we sampled Jesse, the Olympia oyster selected for genome sequencing. Not as big of a specimen as yesterday, but made up for it with video. The oyster was collected in Fidalgo Bay, weighing in at 58.99 grams and 70 mm long. The adductor muscle was selected for genome sequencing, thus quickly rinsed in 10%… Read more »

Big day, big clam

Posted by & filed under Panopea generosa.

Today we sampled the geoduck (Panopea generosa) for genome sequencing. Here is how things went down. It was an early morning for the clam, peaking out to see a glorious sunrise on the porch. From there it was off to the lab. After cleaning the surfaces, Brent sampled tissue. We started out started out targetting… Read more »

Dirty and crude with Oly qPCR

Posted by & filed under Ostrea lurida.

Taking the most decent Ct values, I did the simple and crude calculation, normalizing with EF1 and looking at fold over minimum. Seems to be EF1 data is skewing. Will take a look with actin and also compare delta Ct, using this as a sound reference.

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 »