Posts By: Steven Roberts

Side track with tracks

Posted by & filed under Cgigas DNA Methylation.

Today working on our paper looking at heat stress and DNA methylation I dived deeper into the array data in the search for what should be called a DMR. As a refresher we have tracks from the core that have 1.8+ fold difference (sig) and complementary tracks where there are three adjacents (3plusAdjacent). I made… Read more »

Passing Flanks

Posted by & filed under Ostrea lurida.

A first look at population differences at qPCR primer sites for three population of Olympia oysters Plate 1 (samwhite_112381) included, BMP2, CARM, HSPb11, and PGEEP4. At the bottom is a full list of qPCR primers. BMP2 Limited coverage CARM Better coverage conflicts were ambigs (ie S,W,R) HSPb11 Missed qPCR primer (R did not seem to… 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 »

Quick Carmalign

Posted by & filed under Ostrea lurida.

The first batch of sequencing came into today to verify sequence of Olympia oyster qPCR primers. 1) imported .ab1 files into CLC, 2) trimmed “CARM” sequences 3) aligned to comp7220_c0_seq2

Wayback to just-MBD

Posted by & filed under Cgigas DNA Methylation.

Prior to bisulfite sequencing we did do a couple of MBD enrichment libraries to describe DNA methylation in oysters. Results even were snuck into this perspective. While I am sure there are genome tracks around, I am ending up #doingitagain. In short I took the raw Solid reads, align to Crassostrea_gigas.GCA_000297895.1.26.dna.genome in CLC, exported bam,… Read more »

Shortish list

Posted by & filed under Ostrea lurida.

In selecting qPCR targets from the Oly transcriptome (version 3) I came up with the following list. In general this was done by first focusing on stress response GO slim terms, followed by simple word searches. The table is available for download here The next step would be some joining & file converting to pull… Read more »

A short sequence on short sequence

Posted by & filed under Tutorial.

A quick tutorial to check out primers on NCBI to see what the product size should be and how specific they are. Old school way is just take the primer with NNNs in the middle and blast. TATTCGTTGGAGACTTTATAACCCTNNNNNNNNNNNNNNNNNNNNNAAGGCTTAGAATTGCAAGGTCTATA You will get an output as such…. Scroll down to the alignments…. And look at the coordinates……. Read more »

Splicing around

Posted by & filed under Cgigas DNA Methylation.

Here I am going to see to what degree I can identify differential splicing events that occur upon acute heat stress with the ultimate goal of determing if there is a relationship with differentiall splicing and DMLs. As the Tophat suite was used for RNA-seq, I will start exploring the cuffdiff output. Note all output… Read more »

Hyper-splitting

Posted by & filed under Cgigas DNA Methylation.

With a good two weeks hands-off of the the array data it took a bit of time to get back on target. Following up from last time (per my instruction) I began to delve into how the hypomethylated versus hypermethylated DMLs played out with respect to genomic features. Still not convinced I am convoluting the… Read more »