Lab 12: Gel for Lupine ISSR

Lupine ISSR Gel
Today, we ran out our ISSR PCR reactions on one large gel. The gel is 2% agarose, denser than normal to allow better separation of bands.

Steps for loading the gel were simple and as follows.

  1. Add 1 µL loading dye to each PCR tube.
  2. Load 5 µL of each sample into the gel dry. We did this dry so that samples would not diffuse before all wells had been loaded. The left and rightmost wells contained a 100bp ladder.
  3. we ran the gel at 20 volts for a long time.

I loaded my samples and Danielle’s samples. I also accidentally added one of Daniel’s samples twice; I believe it was sample 4 but it may have been 3-7.

Prof Paul imaged the gel after class.




New Mimulus alignment and concatenation
During lab we also created another alignment of our Mimulus cardinalis sequences. Prof Paul was able to get sequences for several new populations, so we edited the sequences for our given EPIC marker and then included them with the sequences we worked with a couple weeks ago create an alignment with all of them.

We then uploaded our alignments onto Canvas so that we could use other people’s alignments with other EPIC markers. I downloaded Nathalia’s 5525 alignment, Prof Paul’s 5534 alignment, and Jinwoo’s 5551 alignment. I then concatenated all of the alignments to create one set of sequences to build a tree out of.

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