All for Fish, and Fish for All
Welcome Back Fish Friends,
This week the Weicksel Lab got to takeover the @friargram instagram account for Providence College. If you want to check out our cool photos head over to instagram! This basically means we are super cool now.
Weekly Updates:
This week is the 8th week in our 10 week summer research journey.
On Monday, we set up a gel to test out the 3C libraries we made a few weeks ago. Turns out they aren't terrible just not great. We also set up some fish in the mating tanks because like the greedy scientists we are we want more embryos. We got about 300 embryos and proceeded to fix them for 3C because we hope to be able to make new 3C libraries so that we have an easier time identifying loops formed in the DNA. We also set up an ethanol precipitation to extract the DNA from an older genomic DNA sample. We did this to make sure the DNA wasn't degraded and could actually be used.
Tuesday brought more fish matings because we always crave more embryos. We also set up another q-PCR to analyze how well are libraries are working. Most of the q-PCR's we have done are to troubleshoot where problems are in our data and what might be going wrong in our protocol. We suspect that there is something wonky going on with our DPNII enzyme, so we set up a mini 3C digest to test our enzyme against another enzyme called HIND3 and one with no enzyme so that we have a control. Hopefully this can give us insight into what is going wrong.
On Wednesday, we analyzed the q-PCR data from yesterday and our data turned out to work well just a little more troubleshooting to do. We worked to finish our mini 3C by adding a few chemicals and incubating the tubes for an hour. Then we did a phenol chloroform extraction to make sure our tubes only had nucleic acids (basically just DNA). Next we did an ethanol precipitation to have the DNA extraction become very easy. After all this, we ran the data in a gel and it did not give us much insight, so we are marching on with DPNII as our enzyme. We also set up another q-PCR (surprise surprise) to test all 70 of the primers we have designed.
Thursday brought, you guessed it, another q-PCR. We ran a bunch of primers, with other primers to see if they produced a product. If they did, that means that an interaction occurred between those two different primer sites. WE GOT REAL DATA!! It looks like what it is supposed to look like!!! We do need to wait for the information to come back from sequencing before we get too excited, but it's still a victory. We then ran a gel from the q-PCR data, so that we could do a gel extraction and send the samples out for sequencing. We sent off about 11 gel bands for sequencing so fins crossed it turns out okay.
On Friday, the lab waited for results of our sequencing but we didn't hear back yet. We finished up our abstract and submitted it for the SURF conference we will be presenting at in two weeks! Then the lab went out for lunch at DenDen for some Asian cuisine, it sure was delicious!
As always, thanks for swimming by. We hope you enjoyed this weeks installment of the blog. If you have any comments questions or concerns, stop over to our contact page! Keeps those fins peeled for an update next week.
Swim by Again Soon,
The Weicksel Lab
