Jerry Wang, Week 1, Finally starting my summer at UPenn

Week1:

                After a few weeks, I have finally arrived Philadelphia. Things went a bit side track since my kitty scratched me on accident back at home and I need to get vaccinated which would not allow me to go to US till July 18^th. One thing led to another and the result is that I arrived at my lab two weeks later than the plan. But anyways, after the long wait I was really excited to meet my lab member and P.I. My P.I. is currently on a personal vocation in Europe right now and will be back next Monday. Therefore, this week, I worked alongside of Dr. Gunan, the staff member of my lab. First day was always the toughest one. But with the help of Apple map and Upenn’s website, I successfully located Dr. Mason’s lab. The first “task” I had for the lab was making a 0.5 percent agarose gel. It may doesn’t sound hard to all of you who just finished biology but my last biology-related experience was almost a year and a half ago. Thankfully, my lab members were very helpful and patient. With their guidance, I would proudly say that I made a decent 0.5 percent gel on the first day of my lab. Nevertheless, the gel I made broke (maybe melted, I am not sure what exactly happened since my lab members could not find a suitable word to accurately describe the situation) in the middle of the gel electrophoresis process. According to my lab member, they have never seen anything like that before (either way, I kinda made a record in my lab). Luckily, the RNA sample that was running in the gel was not the most important project that we have in the lab, so the melt down of the gel did not cause much disturbance.

Since my P.I. is out of the state for this week, Dr. Gunan is in charge of me. And Dr. Gunan and I received trainings and instructions of how to use Illumina’s miniSeq genetic sequencing machine. On Friday, we were given a lecture about mechanism behind this powerful instrument. Now, on this blog, I will give you guys a brief version of a three-hour long lecture. I still remember what we did back in my sophomore year winter. After extracting samples and running PCR, a few successful sample will be send to Princeton for genetic sequencing. At that time, Mr. Bright only told us they would use laser to sequence the genes. Now, I was able to understand the exact process behind that answer. So, what Illumina does with their sequencing process is that they separate the whole thing into two sections: manual library preparation and automated genetic sequencing. The purpose of library preparation is to transform the DNA sample into desired composition. So, at the end of the library preparation, you would have a DNA sample that looks like this: 5’---index1 sequence---desired sequence---index2 sequence---3’. Then, all you have to do is load the sample onto a bio-chip and put it into the miniSeq machine and the machine will do everything for you (There is a reason for this machine to cost around 100,000 dollars). What happens inside machine is the most amazing part of this process. After loading the bio-chip into the machine, the end of the DNA Sample will bind to the various spots located on the biochip. After that, it will do something called bridge amplification which is very similar to PCR. After multiple rounds of bridge amplification, now you have thousands and thousands of copies of DNA sample in one spot of the biochip. Then, bases with fluorescence attached to it will be load onto the biochip which will then bind to the DNA sample. Laser will illuminate the biochip and different bases will illuminate different colors because different fluorescence is attached to different bases. Since there are thousands of copies of DNA in one spot, that one spot on the biochip will illuminate greatly under the laser. Then, the bases are washed away and bases with no fluorescence will attach to the DNA sample to “block” the already known spot and a new cycle of attachment and laser illumination will begin. After hundreds of cycles, researchers would be able to identify the genetic sequence with a high accuracy. What’s more about this machine is that, it could perform such sequencing method on thousands of samples at the same time. Since there are numerous spots for DNA sample to attach to on the biochip, this design enables researchers to perform large quantity of bioinformatic analysis in a short amount of time. With the help of such powerful machine, our lab will be able to analyze the genetic mutation in various patients with unprecedent speed and efficiency. Such advancement is truly a great support to our lab’s cancer research.