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.
- Send DNA for WGBS
- Extract RNA from gonad samples