We constructed a double digest restriction associated DNA study on Mimulus guttatus. The first step was collecting samples, which we did on two field trips which can be read about here and here . Next, we extracted DNA from the samples… Continue Reading
After double digesting and ligating an adapter to the DNA, we did a test PCR. We did this to test for successful library construction of the samples. First, we made a master mix for the RADSeq using the following: Master… Continue Reading
Our next step for this lab was to do DD-RADSeq. First, we double digested our DNA samples. To do this, we followed the following steps: Double digested 100-1000 ng of high quality genomic DNA with selected restriction enzymes, using a… Continue Reading
We used our DNA template to run PCR reactions (20mL). To do this, we created a master mix with the following solutions and measurements: Ingredients per rxn per 18rxns (mL) ddH20 13.36 240.48 10x buffer 2.00 36.0 MgCl2 2.00 36.0… Continue Reading
Once my DNA was extracted, I prepped it for gel electrophoresis. First, we dotted ~2mL of blue tracking dye on a piece of parafilm. Then, I put ~3mL of each extracted DNA on top of a dot, changing tips every… Continue Reading
First, I labeled 3 2.0 mL tubes with my sample codes (KRS1-3 respectively). I added 3 sterile 3.2-mm stainless steel beads to each tube. Then, I added a small amount of leaf tissue into each tube, cleaning the tweezers between… Continue Reading
I created an alignment of 25 COI sequences from Actinopterygii and my fish DNA barcode sequences, including one Chondrichthyes sequence as an out-group. I did this by searching COI and Actinopterygii/Chondrichthyes in the NCBI nucleotide program in Geneious. I chose… Continue Reading
Using Geneious, we were able to match our fish DNA to DNA in the database. To do this we first copied the reverse sequence from the ‘Fish barcode Reverse Reads’ folder and pasted it into the ‘Forward Reads’ folder. Then,… Continue Reading
On Tuesday, September 24, 2019, we traveled back to Mount Tamalpais, this time stopping near Muir Beach to collect and view samples of mimulus guttatus. We stopped at a natural spring to drink the water and observe the flowering mimulus… Continue Reading
To begin the electrophoresis of PCR product: First, we thawed our PCR tubes We dotted 16 loading dye dots (~1 ul) on a sheet of parafilm We pipetted 3 ul of each PCR product on its own dot We then… Continue Reading
