"R"NA-seq is cool
I've been a bit excited for Mod2 since 20.109 started. Stepping into the class in Mod1 was a bit intimidating--all of the lab procedures were new to me. I wasn't sure what to expect, and I felt like everybody else had already carried out these experiments in their UROPs, while I was left flapping my arms and understanding NOTHING.
So when Mod 2 finally started, I was sorta feeling like:
Fun fact: all I do in my UROP is RNA-seq and data analysis in R.
This isn't to say that I'm an expert--in fact, I've learned a ton so far in Mod 2. I especially enjoyed all of Professor Frankel's lectures, because now I finally understand what all of the R functions I'm familiar with are actually doing :) I'm also used to working with patient samples as opposed to cell lines, so getting to learn about cell culture has been super fun.
However, if my UROP has taught me two things, they're:
1) RNAses are the root of all evil.
2) There is no such thing as too much paranoia.
That being said, here is actual footage of me cleaning our workspace before RNA extraction:
Pretty sure Marissa and I both lost brain cells to ethanol fumes. Sorry Marissa.
And finally, me after after we had successfully reverse transcribed our RNA to cDNA:
Getting started on the R exercises, I was a little excited. I have spent the last 8 months waging a never-ending war upon the R gods, and while I'm far from victorious, I seem to have grappled them into a sort of strangle-hold so that I only have to delete and reinstall R from my computer every couple months (or whenever I try using Seurat). So when we started using R, I'm not going to lie, I was a little pleased. Finally, all of my pain would pay off.
Needless to say, R was not entirely as cooperative as I hoped it would be. Still, it was a heck of a lot easier than if I'd had no experience with it. Also, can we just take a moment to appreciate how BEAUTIFULLY SIGNIFICANT ALL OF THE DATA WAS. LIKE CAN WE JUST TALK ABOUT THOSE HEATMAPS FOR A SECOND. THERE WERE ACTUALLY DIFFERENT COLORS THAT MADE SENSE. WOW. In my UROP, my heatmaps usually end up looking like giant yellow blobs and my supervisor says "oh we need more cells." RIP the dream. RIP significance.
Then, just when I thought things were going great, we got to *cue horror movie music* JOURNAL CLUB PRESENTATIONS.
In all honesty journal club wasn't as terrible as I expected it to be. Honestly I just suck at speaking English in front of people, which is a little sad since English is my first (and only) language. I also suck at speaking English at a rate that is understandable to other people (ie, not at the speed of light). The questions section was actually a lot easier than the presentation part, which I think is probably a good sign because I assume that in most journal club settings you aren't timed, and people stop you to ask questions throughout. This would be helpful because while--after reading my paper ~52 times--everything I said was very clear to me, I had no idea whether I was getting through to the people I was talking to. I kept scanning faces, looking for expressions of recognition. I was getting a lot of blank stares--hopefully that was because the rest of the class was in a food coma, and not because I wasn't making any sense!
Overall Mod2 has been fun so far. While I can't say I'm looking forward to the Mod2 report, I do look forward to putting the pieces of our data together and getting some pretty pictures and a story out of all this hard work!
Best,
Jenna
So when Mod 2 finally started, I was sorta feeling like:
Fun fact: all I do in my UROP is RNA-seq and data analysis in R.
This isn't to say that I'm an expert--in fact, I've learned a ton so far in Mod 2. I especially enjoyed all of Professor Frankel's lectures, because now I finally understand what all of the R functions I'm familiar with are actually doing :) I'm also used to working with patient samples as opposed to cell lines, so getting to learn about cell culture has been super fun.
However, if my UROP has taught me two things, they're:
1) RNAses are the root of all evil.
2) There is no such thing as too much paranoia.
That being said, here is actual footage of me cleaning our workspace before RNA extraction:
Also, me every time our sample tubes touched anything outside of the RNA clean space:
Pretty sure Marissa and I both lost brain cells to ethanol fumes. Sorry Marissa.
And finally, me after after we had successfully reverse transcribed our RNA to cDNA:
Getting started on the R exercises, I was a little excited. I have spent the last 8 months waging a never-ending war upon the R gods, and while I'm far from victorious, I seem to have grappled them into a sort of strangle-hold so that I only have to delete and reinstall R from my computer every couple months (or whenever I try using Seurat). So when we started using R, I'm not going to lie, I was a little pleased. Finally, all of my pain would pay off.
Needless to say, R was not entirely as cooperative as I hoped it would be. Still, it was a heck of a lot easier than if I'd had no experience with it. Also, can we just take a moment to appreciate how BEAUTIFULLY SIGNIFICANT ALL OF THE DATA WAS. LIKE CAN WE JUST TALK ABOUT THOSE HEATMAPS FOR A SECOND. THERE WERE ACTUALLY DIFFERENT COLORS THAT MADE SENSE. WOW. In my UROP, my heatmaps usually end up looking like giant yellow blobs and my supervisor says "oh we need more cells." RIP the dream. RIP significance.
Then, just when I thought things were going great, we got to *cue horror movie music* JOURNAL CLUB PRESENTATIONS.
In all honesty journal club wasn't as terrible as I expected it to be. Honestly I just suck at speaking English in front of people, which is a little sad since English is my first (and only) language. I also suck at speaking English at a rate that is understandable to other people (ie, not at the speed of light). The questions section was actually a lot easier than the presentation part, which I think is probably a good sign because I assume that in most journal club settings you aren't timed, and people stop you to ask questions throughout. This would be helpful because while--after reading my paper ~52 times--everything I said was very clear to me, I had no idea whether I was getting through to the people I was talking to. I kept scanning faces, looking for expressions of recognition. I was getting a lot of blank stares--hopefully that was because the rest of the class was in a food coma, and not because I wasn't making any sense!
Overall Mod2 has been fun so far. While I can't say I'm looking forward to the Mod2 report, I do look forward to putting the pieces of our data together and getting some pretty pictures and a story out of all this hard work!
Best,
Jenna
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