Week 14 – 12/6/17 – Using Paup with our ISSR Analysis

Date: 12/6/17

Location: G04

What I did

In this lab, I inserted the scored ISSR that I made on Text Edit. I saved it as a .Nex file and downloaded the free PAUP program. I had a total of 47 taxa and with 17 scores. After opening the .Nex file with the scored ISSR on the PAUP program, I ran a neighboring Joining/UPGMA analysis on it. This analysis gave me a NJ tree: 

I then ran a bootstrap analysis and it gave me a tree that looked like this:


Week 11 – 11/1/17 -PCR 2 ISSR Plant DNA

Date: 11/1/17

Location: G04

Test Gel

We added 1ul of dye with a micropipetters to our ISSR Plant DNA tubes from the previous class. We then got 10ul of this and placed each sample into a gel for about 1h 45min at 60v. the gel was 1.3x agarose. The primer that we had was OMAR.



We got our plant DNA samples from previous class and made dilutions with it. The samples that I had were PSR 01-05. I micropipetted 10ul of the DNA sample into a 1.5ml microfuge tube and added 90ul of H20 so it was a 1:10 dilution.

PCR Setup

For each Primer, Omar and 1788, we got 2 0.2ml 8-tube strips in each I put each of the Plant DNA sample dilutions. I had 6 tubes, one for each of my 5 samples and 1 extra for the negative. My samples were

PSR 01

PSR 02

PSR 03

PSR 04

PSR 05

With a micropipetter, I put 1ul of each sample into each tube for each of my samples.

For each of our PRIMERS (either Omar or 1788), we made a master mix. The contents of those master mixes were:

ddH20: 15.4ul

10xbuffer: 2.00ul

BSA: 1.0ul

dNTPs: 2.0ul

Primer : 0.20ul

Taq: 0.04ul

Template: 1.0ul

Total: 20ul

We then placed 19ul of master mix into each of the tubes in which they were placed in a PCR machine.