Posts Categorized: Ostrea lurida

Genes (RNA-Seq) on Oly Genome

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We currently have a version (0.0.2) of the Ostrea lurida genome on CoGe. This is 38 scaffolds greater than 80k bp. Below is an effort to map gonad RNA-seq data to said genome. Two male gonad and two female libraries were mapped to the genome using TopHat in Cyverse Discovery Environment. Through the steps… I… Read more »

CoGe on Fidalgo Sibs

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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

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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 »

Data check on Oly BS-Seq samples

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  For the 12 samples Select 4 samples from 1NF gel take 2 Select 4 samples from 2NF gel take 2 Select 2 from gel take 2 Lotterhos M1 M2 M3 Select 2 from the following sent to Katie (do not have to run on gel) NF2 14 NF2 6 NF2 18 NF2 15 NF2… Read more »

Running the numbers

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Today I brought another 16 samples into the DNA extraction pipeline. These were subjected to 30 minute ProK digestion at 60C as opposed to overnight. It became clear the number scheme was complicated thus I converted to 1-32. Will keep this running fwd and cross-referencing. In the future the number scheme will be simpler, but… Read more »

Upon improving extractions

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In an attempt to determine most efficient means to get some high quality DNA from the archived oyster samples – a suite of samples were started out with M1 buffer and ProK. The first ‘unit’ to go through will be the April Dabob samples. For today, I took 16 samples from the Hood canal population… Read more »

A few outliers remaining

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Integrating last bit of qPCR data into master datasheet. This includes 5 runs post 8/15. likely error above – second EF1 was 18s test. CARM Looks nice, corrected… Elong factor Correction is fine, but mechanical reps have some issues As noticed in last batch of analysis these need to be checked at raw data level… Read more »

Finishing out with the mechanical

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Currently there is a pretty robust spreadsheet and over the past few days Jake has cranked through some reps to see how the oysters that were mechanically stressed hold up. Below is how these data are integrated. Currently the 8-10 samples (yellow) have been skipped, but we might have a look. First up is having… Read more »