Nucleic Acid Extraction: the trial runs (Week one)

After getting a tour of the building and meeting all the new interns, I went for coffee with Lydie Herfort to talk about what had been done with the ESP column samples and the soil samples since my visit this spring. We went over some slides and graphs that she had recently made of the sampling times of the ESP and we decided that I should first start on extracting DNA from the recently collected soil samples. Using the FastDNA Spin kit, which I had not used before, Lydie and I extracted the first two samples together to make sure I didn't have any problems using this particular kit . When I had proven myself she sent me off on my own. Once all of the DNA samples were done, nanodroped, and giving nice data it was on to RNA.

I started with test samples from the ESP and Lydie's help because I had never used the protocol before. The first time through it took me two days to complete the extraction although by the time we were done there were minimal mistakes and major changes to the protocol. By the second time through, and  with different test samples, I was able to complete the procedure in half the time while still managing to get nice RNA yield. Nice enough, in fact, that I was able to move on to the real filters that the ESP had collected early this summer. The result for these samples were not as pretty as they were for my test samples but I have been informed that the results were average for most of RNA extraction that Lydie preforms so that is good news. 

Because for the first half of the protocol we do not use a kit, RNA extraction are longer, more tedious, and easier to mess up on. Although for these reason RNA extractions are also a little more entertaining since it requires much more thought process. Since I have spent a good portion of my scientific life extracting DNA it is also enjoyable to get to do something new. The worst part of the RNA extractions is having to continuously transfer the supernatant from one tube to another and all the wait time as the samples are spun or left to incubate. Though for the most part I can line up the treacherous one hour weight time with lunch so I don't feel like I am wasting too much time waiting for the samples to process before I move on to the next. 

Once all the nucleic acid is extracted from all the samples  we can then preform qPCR on them. Hopefully that will be next week.