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 the foot and adductor muscles. These tissues were steriley removed and then rinsed in 1% bleach, followed by Nanopure water. This tissue will be used for genome sequencing as we predict least amount of associated taxa.
Remaining tissues were taken, primarily for RNA-seq and divided into two boxes.
Tubes were labeled on cap with tissue type.
Here is what Box 1 looks like.
Box 2 looks the same however it does not have a heart or style sample.
The only surpise was in sampling, labial palps were identified after we had already sampled a pair.
Samples were run on 1.0% agarose, low TAE gel stained w/EtBr.
Ladder used was O’GenRuler 100bp DNA Ladder (Thermo-Fisher).
No sample was loaded directly next to ladder to facilitate excision, if necessary.
Each sample was accompanied by a no template control (NTC).
The ehrlichia universal primers (EHR) and the universal 18s (18s) primers are the only two primer sets that do not have contamination present in the NTCs.
Excised the EHR band and purified with Ultrafree-DA columns (Millipore). Purified DNA was stored @ -20C and will be used for cloning/sequencing next week.
Have already ordered additional primer sets of those above that are contaminated. Will re-run the PCR with those new, sterile primer sets when they arrive to obtain a larger product (the EHR amplicon is only ~350bp).