Just got these photos of a couple organisms that are thriving in the aquarium tanks that we helped set up as part of the Aquarium Project. Stay tuned for sequence data one of these days…
Today was the final presentation by the students working on the aquarium research project. Alex, Lakshmi, Sabreen, Andrew, and Kevin all talked about their recent work using QIIME to analyze the 16S sequence data from the project.
Their presentations, along with my introduction can be found here.
Now we need to take some time and really dig through the data to see which samples we should take out of the freezer and analyze in order to create the most useful dataset to look at community succession in these coral ponds.
So we’ve done our data collection, we’ve done more PCR than we could ever imagine, and we finally got our sequences. Now what? We analyze our data using Qiime, a software that will help us see connections between our microbe data. Qiime is useful since it can handle the large amounts of data we’re throwing at it, something most other programs would crash just thinking about. As someone with average knowledge of computers, it’s entirely intimidating learning something based on programming from scratch, but it has also been a great learning experience. Now off to play with terminal and find some meaning in these strings of letters…
Seven months after starting the sample collections we finally submitted our pooled 16S library today for sequencing. We have somewhere around 90 samples from a few different types of aquariums and our community succession experiment. Now time for everyone to learn QIIME!
I’m sitting here in the lab looking at our google doc and it’s looking pretty good! We only have a few final dilutions to do and we’ll be on our way to sequencing! I’m waiting for David to come back from lunch so he can update me on the next steps.
I’m excited for what’s to come!
A few of the PCRs last week didn’t work so I’m finishing up the last PCR B’s right now that we’ve had to redo and then all we have to do is Gel confirmations. If I counted correctly there are 24 confirmations to do. I would like to do one now, but I have to catch the bus in 30 minutes and I wouldn’t finish in time 😦 I plan to come in on Friday and possibly Thursday as well and hopefully as a group we can completely finished and get our samples in the sequencer by the end of the week!
Then comes the hard part! Data analysis. I learned a lot about this portion of the project while I was preparing my part of the lab meeting presentation a few weeks ago so hopefully that knowledge helps me understand what’s to come. Like most things, I’m sure it’s much easier said then done!
Just an FYI that Holly and I received a grant from Amazon for a bunch of cloud computing credits for the aquarium project. This will allow us to run all of our various 16S analyses for free on their servers.
Today I did 32 PCR B’s. It may sound like a lot but PCR B’s are extremely easy so it went by pretty quick. I also messed up on updating the google doc and had to throw away three PCR A’s that I did last week. Not a huge deal, but kind of annoying!
Right now we have a lot of Gel Confirmations to do. I counted and there’s 48. So to whoever is in the lab next… have fun! 😉 I’m hoping they all come out good so we can get some sequencing done!
Today I primarily focused on reorganizing some of our stuff. First, I went through our two boxes of extracted DNA and put them in numerical order by sample ID. I think at one point they were in order but with all the PCR redos they’ve gotten quite mixed up and I’ve found it hard and annoying to find the right samples. The first box has any samples under #160 and the second box is any number above #160. The samples are also in order in each box, but I have a feeling that won’t last long 😛
Next I reorganized our PCR box. This didn’t take long. All I did was check to make sure all the forward and reverse primers had stuff in them, replaced a couple empty ones, and put them in order in the box. I did have one concerning discovery though: One of the primers said F2 on the side but F3 on top. I threw that tube away to avoid further confusion.
Lastly, I went through each box of samples from the minus 80 degree freezer and wrote the sample ID range of the samples in that box. For example I would have written “#’s 200-300” for a box with all samples between 200 and 300. It was a bit difficult to write on the boxes because they were so cold!