November 13 Getting Better

In the lab, today was another routine day. In the morning, I prepared my samples and ran my PCR. For the afternoon, I ran my PCRed samples through the electrophoresis chip and got some less than perfect results. This came as a result of problems with the ladder.

Time for some explanation. The electrophoresis machine measures how long it takes the sample to pass through the gel matrix. However, before the sample runs, the "ladder" runs through electrophoresis. The ladder is a mixture of molecules that vary in length. The machine and the ladder are produced by the same company, so the sizes of the molecules are already known before they're run. Since they know the 50 basepair (unit of measurement for DNAs and RNAs) group of molecules take  roughly 43 seconds, they can conclude the unknown length of the sample based upon how long it takes.

The problem was that my leader was off, so the sizes that the machine was given weren't accurate. As a result, I can't use this data. However, there is a bright side. I saved my samples and I can run them again (likely tomorrow because indeed to run some with Xiaolu's samples that aren't ready yet).

But more importantly, since I've gotten all 3 cDNAs into a good ratio with the competitor molecules, I should hopefully start cranking out data much more rapidly now. I will start running larger (12 samples per test) tomorrow.

During my down time, I looked through the paper that Erin sent me. I can't really explain exactly how they did it, but Tom and his colleagues found parameters that allow for the whole transcriptome sequencing to be more reproducible across different labs and for it to be done in extremely less (reduced roughly 10,000-fold) number of reads. I'll try to understand it more so that I can tell more about it.