Week 3- Starting DESeq2 and Wet Lab Shadowing

Arnab M -

Hi guys,
It’s Arnab and this is my third weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing.

Picking up from last week, we successfully ran STAR Alignment on our data files and successfully produced BAM files, which are a certain type of data files in Bioinformatics that contain the raw data of genome sequencing and contain a version of the Sequence Alignment Map files that we will be using in the next step of our workflow (attached in the first and second pictures). Now that STAR Alignment is complete we will continue on to our next step, DESeq2. This is where we take our data files produced in STAR Alignment and compare differentially expressed genes within different experimental conditions through an R Studio coding package. This week I’ve been reading extensively on DESeq2 and what is happening behind all the code and computer screens. In short, DESeq2 will help us visualize and analyze all this normalized data we have been working with since the start of this project and prepare us to move through our workflow and figure out if PNPLA7 is a gene that we should be interested in.

In other news, I got to shadow another member of Dr. Kruer’s lab in the wet lab and her work on drosophila. I’m unable to provide any pictures due to confidentiality reasons, but the lab has a multitude of high-tech equipment and ongoing experiments relating to CP. In my mentor’s drosophila experiment, I got to participate in her drosophila movement speed measurements test and move the larvae to prepare for her future fly crosses.

This week brought a fantastic new dimension and perspective to research and how many people, resources, and lives are involved in this incredible process of fighting CP. I’m excited to see what next week brings!

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    James Kittredge
    Amazing work, Arnab! What is your advisor studying in the drosophila experiment?
    March 4, 2024 at 8:45 am - Reply
    arnab_m
    Thanks for the wonderful question! My advisor is studying the difference in movement speed of specific drosophila. The control flies are normal lab-cultured fruit flies, while the experimental group is special flies with a gene of interest completely removed or inhibited. Here she can test whether this gene of interest affects movement and contributes to the drosophila's movement disorder as it does in human CP. Hope this answers your question!
    March 5, 2024 at 9:36 am - Reply

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