Within my study with Sarah, we explored many different possible avenues for our research, as Sarah wanted to provide me with an extensive experience to really understand what it took to plan out an experiment. We initially talked about a kelp gametophyte experiment that we wanted to look into, since I have an interest in kelp, but it became difficult rather quickly when it was time to obtain the gametophytes, as kelp has a certain reproductive period that made harvesting the spores from the gametophytes rather difficult. This brainstorming period lasted for about a month and a half into the beginning of winter quarter.
We decided to then switch from that idea to Sarah’s current coral research that she has been doing, which involved taking her previously leachate exposed coral samples (Montipora capitata) and doing DNA/RNA extractions to obtain these samples that we could send for sequencing to determine differences in gene expression among the groups of corals that were exposed to different levels of leachates.
It took a while to develop the correct protocols and obtain the necessary lab materials to get started on our extractions, so we spent a lot of our time together talking through the goals of our experiment and how we wanted to pull together protocols from different sources to obtain the best method of extracting DNA/RNA. We officially started our extractions at the end of April, and we currently have 20 samples extracted, all with varying amounts of RNA and DNA collected. We’ve ran these samples in the Qubit, and many of them need to be diluted before they can be sent for sequencing, since they are over the allocated threshold for sequencing purposes, so we have yet to send them off for sequencing nor have we found any information regarding the gene expression differences within these groups yet.
However, we did notice as we continued our extractions that some samples were yielding large amounts of DNA and then yielding low amounts of RNA, which prompted us to investigate the potential relationship that these two may have with one another. We decided to do a Wilcoxon paired sample rank test, because each row of DNA and RNA were extracted from the same sample. We wanted to know if our Dual extraction method is biased toward optimizing yield for DNA or RNA, or if there is any trend at all.
If you go to my Extraction Data post, you can find out about our results between this yield difference of DNA and RNA.