Grace’s Notebook: May 3, 2018, Crab Meeting and Bioanalyzer

Crab Mtg #3

Today we had Crab Mtg #3. I presented my little .csv file )20180502_seq_subset.csv) that contains all the samples that RNA was isolated from and for which there was 20 ng/µL or more of RNA in the final samples.

I need help figuring out how to create a file that only contains those samples that have three samples per crab. Here is the GitHub Issue (#244). I see that Sam gave some instructions, so I will try those out tomorrow!


Sam showed me how to run some samples on the bioanalyzer! (MarScience bldg, Seeb Lab).

I ran it on tube numbers 274 and 401 (FRP 6210). These two tube numbers correspond to a crab (FRP 6210) for which I only have two successfully isolated samples. In other words, they are extras.

The bioanalyzer did not go well. We think this is because the RNA marker is too old. So I will try again tomorrow using the RNA marker from the new kit, while using all the other reagents from the old kit, becuase those all worked still.

I will also grab the data from that failed run and include in this post.

Tomorrow’s plan:

  • Work on data org. some more
  • Edit and publish Crab Mtg #3 recording (as DecaPod S1Ep7)
  • Run the bioanalyzer on those two samples again, using the new RNA marker
  • (Work on my presentation for my FISH 511 class – I present on Monday on “Oceanic Orgies”)

from Grace’s Lab Notebook

Grace’s Notebook: May 2, 2018, RNA Isolation and Data organization using R

RNA Isolation

I did these samples:

Tube 73, because I didn’t do it yesterday (accidentally did 37 instead)
Tubes 335 and 497 because they are the final two samples for the crab from tube 37 (FRP 6127)
Tubes 107, 311, and 504 because I needed a replacement infected, ambient crab

Qubit results:

Tube 504 has a comparatively high RNA concetration (15.5 ng/µL). I will ask in the Crab Mtg #3 tomorrow if this is ok/ what it could mean.

Data organization using R


So, what I wanted to do was to combine two files based on the common column, “tube_number”.

The files:

  • contains the Qubit results for ALL of the samples I have “isolated” RNA from


  • contains all of the samples (from crabs that survived the experiment – three samples/crab) that I did the RNA isolation protocol on

I used this R script:

And I ended up with a new file that contains all of the samples that had a final RNA concentration (in 50µL of sample) of 20 ng/µL or higher:
Sample subset file


The subset file has too many samples listed because it has some samples that are missing the third in the set (by set, I mean the three samples that each crab has). Also, it is excluding some of the samples from the warm treatment tanks. This is because some of the warm treatment tanks had “Out of range” or “0” RNA according to the Qubit.

I’m not sure if we want to send the warm treatment tank samples that have “Out of range” Qubit results. Will discuss during tomorrow morning’s meeting.


  • Bioanalyzer with Sam on a couple samples (before meeting)
  • 11am crab meeting
  • work on data sheets, DecaPod FAQ Pt 2 and Crab Mtg #3

from Grace’s Lab Notebook