Gels and Beads
After a 3-day weekend, on Tuesday we were all well-rested and ready to come back to the lab! We continued working with our ancient DNA extractions. We had already added a short DNA sequence to one end of the DNA fragments (i.e. an adaptor) that we can use later to amplify the DNA (that’s stage 3 of the single-stranded library prep–see previous post). On Tuesday we continued from Stage 4 all the way to Stage 7 (listed below and explained in the figure).
Stage 4: Attaching DNA to magnetic beads (using the adaptor we aded on Friday)
Stage 5: Copying the DNA (new copy shown in red below, making it double-stranded again)
Stage 6: Cutting the strands to be the same length
Stage 7: Attaching a second adaptor to both strands and separating the new copy (in red below) to use later—this is our ancient DNA library!
We then ran a quantitative PCR (qPCR) to find out how much DNA we had to be able to optimize the next reactions.
In the modern lab, we learned how to do gel clean-ups of the Long-Range PCR we had done on Friday.
This was a long day of lab work and by the end of it we were all tired and ravenous. So on the way we went to our favorite Turkish fast food restaurant to get doners and it felt like the best meal ever because the food came quickly and it was very yummy and filling.
On Wednesday morning, we were anxious to see our qPCR results because that would tell us if our library preparation was a success or not. It was!
We then proceeded with our library prep from Stage 8 where we amplified our library. After amplification, we purified the amplified libraries using MinElute and determined the fragment size distributions and concentrations of the libraries using Bioanalyzer with the DNA 100 chip. Next, we quantified the concentrations of our library using a Qubit and we were done for the day.
(P.S. When you read Jacob’s post, I did not insist we don’t buy tickets for the train to Berlin! Jacob just won’t admit that he couldn’t figure out how to use the ticket machine…)