WGBS Samples Part 7

Final quality check

After talking to Steven, we decided that I would drop samples 7 and U3 since they barely had any DNA and attempt to sequence the remaining eight samples. That would give me a balanced design with four samples per treatment. In case my two samples that have less than 500 ng of DNA cannot be sequenced, I will have four treatment samples and two control samples. Since this is still an exploratory study and I don’t know if there will be any effect, it may be okay to re-extract DNA. Definitely makes my lab life easier too.

The sequencing facility will do library preparation, so I just wanted to check DNA quality for the samples I precipitated. I created 1:10 dilutions of each sample with 1 µL of DNA and 9 µL of DNAse free water. I ran these dilutions on the BioAnalyzer with some C. virginica samples.



Figures 1-2. BioAnalyzer results (bottom row).

I still have a decent amont of high molecular weight DNA! Sample U2 has a lower peak than the others, so that will be something to consider for library preparation. To determine if these samples will even be considered for library preparation, I emailed Genewiz and Zymo. Both facilities told me they could try their best with these samples, but the Zymo rep sounded way more confident about yield.

Going forward

  1. Send DNA for WGBS
  2. Extract RNA from gonad samples
Written on August 11, 2020