Hi everyone!
Hope that everyone’s summer in the lab is going well! This past week (the week of the 11th, sorry by last entry was a bit delayed) was my fourth week in the lab. I can’t believe that I am already more or about half way done my time with my lab, the days are flying by! This week was slightly more of a down week in the lab, running the standard procedures for new groups of embryos. (It was also a shorten week for me because we had a last minute family issue that I needed to care of, which required a shortened day on Wednesday and off on Thursday.)
This week on Monday, I started out the week with another day of imaging. This time, however, I imaged the 24 hpf embryos. It took a large part of the day, but I ended up recovering 20/25 embryos from the in situ for imaging. Since the 24hpf embryos are more developed and have more of a defined figure (aka look more like an actual fish), they were in my opinion, much easier and much more interesting to image than the 18 hpf. I honestly don’t know why, but personally I guess it made a different when they were more developed, maybe because they looked prettier (and more recognizable) in the pictures, but also because they were much easier to position. After I finished imaging in the afternoon, I started the first part of the DNA extraction for the other half (#9-19) of the 18 hpf embryos. Because the third step in the procedure for the DNA extraction is to incubate the embryos over night in the water bath, I wanted to make sure that I started today, so that I would have the DNA ready tomorrow.
On Tuesday morning, I came in and got right to work on the rest of the DNA extraction procedure for the last half of the 18hpf embryos. Once I had extracted the DNA, I measured the DNA on the Nanovue. Because I finished a little earlier than expected, I was able to go with Abby and Patrizia to the Influx machine at Penn. The Influx is very similar to the cell sorter (JACS) that we used last week, but it sorts the cells more gently, so that hopefully we will have cells on the slides after the cytosine and fixes the problem that we had last week. Having never used the Influx before, we just used a control group for the cell line, lmo2, that we were sorting, to make sure that it gave us cells at the end that were visible before we ran the actual experiment. After we took the cells sorted from the Influx to the cytospin, we were so happy to see that there were beautiful, clear cells on each of the slides!!! I spent part of the afternoon with Patrizia looking at the slides and the morphology of the cells. It was awesome to see so many different types of blood cell lineages at different stages of maturation under the microscope. I honestly could have spent hours looking and identifying all the cells, I thought it was that interesting. Also, it was so great to know that the Influx worked to sort the cells and gave us the results that Patrizia wanted! In addition to imaging the slides, I also ran the PCR for the samples that I did the DNA extraction for that morning so that they would be ready for sequencing this week.
Because of a family issue, I only came in Wednesday for a few hours before heading home. In that time, I ran a gel with my PCR from yesterday and then started to cut some of the bands from the gel for purification. Patrizia said that she would happily finish anything that I didn’t get to so that the PCR could be sent for sequencing. Unfortunately, when Patrizia went to finish cutting the gel, she noticed that the marker and some of the PCR products had faded and that the sequencing would most likely not go well. Since the results from the first 8 samples came back with an unreadable sequences anyway, we decided that it would just be better to re-run all the PCR for all 19 samples of the lmo2 18hpf DNA.
All day Friday was focused on re-running the PCR for all 19 samples of the lmo2 18hpf and then running the samples on a gel to prepare for sequencing. Also, because something might have been weird with the gel that I prepared (might have been too cold or hot when I added the ethidium bromide), Patrizia wanted me to watch her prepare the gel to see if I noticed anything different. On a different note, this is the first time that I have mentioned it, but because CHOP has so many summer students in labs across the campus, they have put together a really nice seminar series that features all types of doctors from all different departments at CHOP. Although most of the kids who attend the lectures are in college, I am lucky enough to attend the weekly sessions on Fridays with Abby. Each seminar runs about an hour long, with each doctor talking a little bit about their field and then talking a little bit about their journey that led to who they are now, along with giving career advice. The talks are always so informative and it is really cool to get a background in all different types cancer research that are going on at CHOP and the innovative techniques that so many of these doctors are creating and using to make huge strides in the cancer community. The career advice is also extremely valuable, especially for someone who is only in high school! That afternoon, I helped Abby with some imaging of a specific transcription factor, cmyb, in the MLL-GAS7 fish. Patrizia and I also prepared a gel to run my PCR, but unfortunately when I went to take out the gel from the model, it ripped. Because it was almost time for the lab meeting and we wouldn’t get the sequences until Tuesday regardless of if we ran the gel today or Monday, we decided that it would be better to not rush and finishing running the gel on Monday. Friday finished up with a lab meeting, where I got to learn more about the research that the other post docs in my lab are conducting and Abby and I also did a short presentation about our research this week!
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