WGBS Samples Part 5
Checking samples on the BioAnalyzer
I need to conduct an isopropanol precipitation with certain samples but before I do that, I figured I’d check the DNA quality on the BioAnalyzer. In case there were any samples with really bad quality, I could then replace them with different samples or decide to reduce my sequencing experimental design. Looking at the sample concentrations, I decided to create 1:10 dilutions so the input DNA would be less than 10 ng. I then went to load the samples on a BioAnalyzer chip. I had to discard two chips in the preparation process: the syringe popped open before the one minute mark with the first chip, and I ran out of the gel dye matrix when working on the second chip. I needed 9 µL more of the gel dye matrix, but I wasn’t sure if I could preserve the gel dye matrix in the fridge or if it would be okay while it sat outside for 45 minutes as I created a new matrix. To be safe, I tossed that chip.
I prepared a gel dye matrix with the new reagents that got delivered on Friday, and vortexed the matrix for 15 minutes at 2300 rcf. Then, I prepared and ran the chip! I’m 2/2 on successful chip runs today.
Figures 1-2. Electopherogram and gel for C. gigas gonad DNA samples.
Most samples have peaks around 2000-3000 bp. Sample UK-04’s peak is ~1000 bp, so I’m unsure if that will be an issue. I’ll continue with the isopropanol preciptation for 07-12, 11-T4, UK-02, UK-03, and UK-04, and then check quality again.
- Complete isopropanol precipitations
- Prepare dilutions and run them on the BioAnalyzer
- Extract RNA from gonad samples