Arnab M's Senior Project Blog

Project Title: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing
BASIS Advisor: James Kittredge
Internship Location: University of Arizona Department of Child Health, Kruer Laboratory
Onsite Mentor: Peter Skidmore



Project Abstract

Cerebral palsy (CP) is a prevalent rare pediatric neurological movement disorder, with an incidence of 2-3 per 1,000 live births. While most cases are due to environmental factors like asphyxia, trauma, and infection, recent discoveries using revolutionary RNA genome sequencing technology provide researchers with a cost-effective way to look into the genetic causes of CP, leading to the discovery of many new causative genes (TUBA1A and CTNNB1). Recently, Dr. Michael Kruer’s lab has identified PNPLA7 as a novel gene of interest for CP through whole exome sequencing. This research project aims to investigate the impact of damaging mutations in PNPLA7 on gene expression levels related to CP using RNA-Seq data analysis. The project seeks to unravel affected molecular pathways and explore potential implications for patients with PNPLA7 mutations. By collaborating with professionals at Phoenix Children’s Hospital and the University of Arizona College of Medicine, this research endeavors to contribute to the cutting-edge field of bioinformatics in medicine and work towards improving the lives of children affected with CP.

    My Posts:

  • Conclusion to Exploring The Genomic Effects Of PNPLA7 Mutations On Cerebral Palsy Through RNA Sequencing

    Hi guys, my name is Arnab Misra and welcome to my final blog post about my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing. Today I will not be discussing the technical details of my project, rather the implications and bigger picture of Cerebral Palsy Research and... Read More

  • Week 10 – Presenting the Project

    Hi guys, It’s Arnab and this is my tenth weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing. These past weeks have been incredibly stressful but productive. As we have finished the entirety of the research and analysis work from this research project it... Read More

  • Week 9 – Results and Conclusions

    Hi guys, It’s Arnab and this is my ninth weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing. This week was incredibly exciting as the accumulation of all the hard work done in this research project yielded promising results. Through our two primary Downstream... Read More

  • Week 8- Data Analysis Continued

    Hi guys, It’s Arnab and this is my eight weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing. This week we took a deep dive into the other part of Downstream Data Analysis in RNA Seq: Gene Set Enrichment Analysis (GSEA). GSEA serves as... Read More

  • Week 7- Data Analysis

    Hi guys, It’s Arnab and this is my seventh weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing. This week I spent almost the entirety of my time wrapping up the bioinformatics coding part of my research project by taking on the daunting task... Read More

  • Week 6- Introduction to Gene Ontology and Overrepresentation Analysis

    Hi guys, It’s Arnab and this is my sixth weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing. This week at the lab I was introduced to this new term: Gene Ontology. Gene Ontology (GO) is a powerful resource utilized in bioinformatics and computational... Read More

  • Week 5- One Step Backwards, Two Step Forwards [Re-running STAR Alignment and HTSeq]

    Hi guys, It’s Arnab and this is my fifth weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing. As expected from the start of this project there would be setbacks, trials, and tribulations; however, no obstacle should ever separate you from your goals especially... Read More

  • Week 4- DESeq2

    Hi guys, It's Arnab and this is my fourth weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing. I was ecstatic to re-transition back to the lab, jumping right into all my last week's assigned readings surrounding DESeq2. We tested my knowledge by tackling... Read More

  • Week 3- Starting DESeq2 and Wet Lab Shadowing

    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... Read More

  • Week 2- STAR Alignment

    Hi guys, It’s Arnab and this is my second weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing.  Last week my mentor and I designed a complete workflow for the early stages [FastQC→ MultiQC → STAR Alignment] that we’ve been successfully following. As the... Read More

  • Week 1- FastQC

    Hi guys,  It’s Arnab and this is my first weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing.  Today was my very first day in person at Dr. Kruer’s Lab at the Arizona Biomedical Campus in Downtown Phoenix. I got the incredible opportunity to... Read More

  • Introduction to Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing

    Hi guys, my name is Arnab Misra and welcome to my blog about my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing. Genetic disorders have long plagued our society since the beginning of human existence. However, in the last decade,  rapid developments in the fields of genomics,... Read More