Swabs to Genomes: Week 6 (Discuss Library Prep)

(This post was written by group #2 as a writing assignment)

IMG_2638 Since we were about half way through this quarter, the activity we did this past week was to summarize all the experiments we have performed so far, list the consumable materials that were used, and any questions or concerns that may have arisen during those weeks. We drew pictures to summarize it on the whiteboard. Ashley then answered all of the questions, and added some of the materials we may have missed.

Next, we answered tough questions about library preparation such as what enzymes were used,  and explaining steps like adapter ligation, PCR and quality control. Since Ashley and David worked on this part of the research, they wanted to make sure we understood what they did. Ashley put up steps 0-7 on the whiteboard and wrote a few challenging questions underneath each step. She assigned three rows of students to answer two steps of the qIMG_2642uestions as best as we could. When everyone was nearly done David went through each question and also corrected the ones we did not answer correctly so we had a very good understanding of the process.

The challenges we encountered were answering the questions about library preparation which was done by Ashley and David. The PDF instructions provided for us a reference were fairly arbitrary. One question we had in the step 5 of the PCR was “how many cycles did we set the thermocycler to?” which David confirmed that it depends on how much material you start off with and how much you want to end up with.
So far, this class is much more challenging than anticipated from a 2 unit class. I am having to learn techniques that I don’t even know where to start learning how to perform. I do think I am learning much more in this class than I have in previous lab settings, and I appreciate the learning experience. Every student should take this class to really understand what it takes to do this kind of work.IMG_2644

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David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at UC Davis. David works at the intersection between research, education, and outreach in the areas of the microbiology of the built environment, microbial ecology, and bacterial genomics. Twitter