Kaitlyn’s notebook: measuring geoduck

Today I finished measuring geoduck. I will calculate some basic stats with them tomorrow. All ROI sets are on Emu, and measurements can be found here.

Sam’s Notebook: TrimGalore/FastQC/MultiQC – C.virginica Oil Spill MBDseq Concatenated Sequences


Previously concatenated and analyzed our Crassostrea virginica oil spill MBDseq data with FastQC.

We decided to try improving things by running them through TrimGalore! to remove adapters and poor quality sequences.

Processed the samples on Roadrunner (Apple Xserve; Ubuntu 16.04) using default TrimGalore! settings.

After trimming, TrimGalore! output was summarized using MultiQC. Trimmed FastQ files were then analyzed with FastQC and followed up with MultiQC.

Documented in Jupyter Notebook (see below).

Jupyter Notebook (GitHub):

Ronit’s Notebook: qPCR Assay Trial Run

Today, I worked with Sam to do a trial qPCR assay using some old juvenile oyster samples from a graduate student’s experiment. We used 8 cDNA samples (4 control, 4 CO2 exposed) and looked at 3 different genes: elongation factor, HSP90, and CYP1A. Sam showed me the calculations for creating a 15 microliter master mix and I created master mixes for the 3 gene targets. For each master mix we added: 5′ primer, 3′ primer, qPCR master mix, and water. I’ve attached a picture of our calculations below:


We decided to multiply each volume by 8.8 (10% greater than the actual needed amount) in order to ensure that we had enough master mix. I then transferred 15 microliter of each master mix to the well plate along with 5 microliter of cDNA sample. 3 negative control samples were also kept on the plate in which I put 5 microliter water instead of cDNA. Note: we initially forgot to account for the negative control samples in our master mix calculations, so we had to go back and add additional master mix volume to the original solution (which is what the red numbers on the right indicate).

We then took the well plates to the qPCR machine where Sam walked me through the protocol for the amplification phase as well as the theory behind it. We left the samples running (the machine stated that it would take approximately 1hr 30 minutes to complete) and will check the curves when I come in to the lab next.

Samples were kept on top of the box labelled 1 in the 2nd freezer: