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.

Going forward

  1. Complete isopropanol precipitations
  2. Prepare dilutions and run them on the BioAnalyzer
  3. Extract RNA from gonad samples
Written on August 5, 2020