West Coast Green Crab Experiment Part 35

Testing out new SMC primers

We got new primers! I ran a PCR and gel with the new SMC primer set to see if that will solve my contamination issue. We thought that our current SMC primer set was contaminated because the COI PCR and gel came back clean.

Screenshot 2024-02-05 at 4 56 14 PM

Figure 1. Gel for PCR product for samples 35, 163, 11, 185, 70, 98, 117, ladder, 126, 176, 168, extraction blank, 2/5 SMC PCR blank, 1/22 SMC PCR blank.

Welp, the new PCR blank is coming back contaminated. When Vanessa and I did our COI test, we tossed everything into the UV crosslinker. I didn’t do that this time, so perhaps I need to do that moving forward since there is so much crab processing happening in the lab right now. Sara and I also talked about how Chelex DNA product is pretty dirty and degrades quickly. So my next step is to clean and put everything in the UV crosslinker, then run a PCR with the new primers with some of my samples, as well as some extra DNA Sara has from other green crab Chelex extractions she’s doing. I can then run a gel with the PCR product from tomorrow, my PCR blank from today, and my PCR blank from 1/22 to compare.

Going forward

  1. Work with Vanessa to leave decontamination station
  2. Work with Vanessa to finish extracting respirometry samples
  3. Work with Vanessa to continue with Chelex extractions, PCRs, and gels for TTR crabs
  4. Perform Qubit assay with any sample consistently not showing up on a gel
  5. Genotype remaining samples
  6. Examine HOBO data from 2023 experiment
  7. Determine best statistical approach for analyzing performance data
  8. Demographic data analysis for 2023 paper
  9. Update methods and results of 2023 paper
Written on February 5, 2024