Kennedy Clark
MIT Department: Biological Engineering
Faculty Mentor: Prof. Ed Boyden
Research Supervisor: Debarati Ghosh
Undergraduate Institution: North Carolina Central University
Hometown: Charlotte, North Carolina
Website: LinkedIn
Biography
Kennedy A. Clark is a senior Biomedical Sciences honors student at North Carolina Central University. Her interests lie in cognitive and behavioral neuroscience, and she plans to pursue an M.D./Ph.D. to focus on mental illnesses and learning disabilities to help further innovate current treatments. Within her home institution, she works to understand the effects of ethanol on the adolescent brain. In the summer of 2023, through the Duke – NC Central Alcohol Research Education program, she discovered that sex had no effect on Cyp2e1, a liver enzyme, during binge drinking.She is now part of Dr. Ed Boyden’s laboratory within the Brain & Cognitive Sciences Building. She aids in increasing the capabilities of Expansion Sequencing, a technique that creates high-resolution maps of RNA and views gene expression differences within cellular and tissue samples. She serves as a co-captain of NCCU’s women’s volleyball team and enjoys drawing, exploring, and video games.
Abstract
Optimizing Reverse Transcription Within Expansion Sequencing To Increase The Untargeted Expansion Sequencing Yield
Kennedy Clark¹, Debarati Ghosh², Edward Boyden³
¹Department of Biological and Biomedical Sciences, North Carolina Central University
²Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
Expansion Sequencing (ExSeq) is a newly developed technique that involves physically expanding an intact tissue sample that has been chemically immersed in polyelectrolyte gel in order to perform in situ RNA sequencing. This allows for the genetic activity to be analyzed when it could not be reached before. The UnTargeted (non-specific mapping of genes) ExSeq provides a broader scope of sequencing RNA in an unbiased way and has the capability to reveal thousands of genes within a sample concentration. However, within the current UnTargeted ExSeq protocol the reverse transcript (RT) step must relinquish to padlock probes binding on targeted RNA templates, although RT is a process necessary in biochemically modifying anchored RNA’s into sequence-able in situ forms (21’). The aim of this project is to improve the UnTargeted ExSeq protocol for unbiased nanoscale sequencing via optimizing the RT step and increasing the specificity of the in situ library. An ideal capability of those technologies would be to expand its tissue range to those outside of the lungs and brain.
