Meetings, Protocols, and Eggspensive Machines! – Week 1 Update

After a brief summer, last week I made my way back to the ‘burg. My summer of birds began with a meeting with my advisor and we established a general plan for the next 10 weeks. Since this summer I will be continuing work that I have already been working on during the school year, it didn’t take long for my Natalie, my lab partner, and I to get back into the swing of things.

We started our week by taking stock and doing some inventory to make sure we would be set for the summer. We looked through our lab supplies and made sure we had all the equipment and reagents that we are planning on using in the weeks to come. Of course, we couldn’t recall all of the materials from memory so this required us to thoroughly go through our protocol. We are planning on using the same RNA extraction protocol as others in the lab, perhaps with a few minor adjustments to tailor the quantities and ratios to our samples, but we soon realized that some of the steps in the current protocol are not completely clear so we spent some time editing and adjusting the protocol as well.

Our main constraint this week was that although we have used the equipment in the molecular core lab, we have not been formally trained to use it by ourselves so our research could not continue until we had been trained. We prepared samples and with them, learned how to use some fancy equipment (like the MagMax machine) which we will continue to use for the rest of the summer.

A typical “run” involves selecting samples, mixing them with TRIzol to stabilize/preserve the RNA, extracting that RNA using the protocol and fancy machines mentioned above, and finally running the extracted RNA through a spectrophotometer (to check RNA purity) and running a gel (to check quality).

Using the NanoDrop! #eggspensive

Using the NanoDrop! #eggspensive

Our first two runs yielded good RNA but unfortunately also contained a lot of DNA which we don’t want in our samples. We were very happy to see that we had extracted RNA successfully but now we have to reduce the amount of DNA. Thus, our goals moving into next week are to review our protocol to see where the DNA is coming from – did we remove it incorrectly or was it shredded and incorporated into the RNA? – and to fix this issue by making adjustments.