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Hippocampal transcriptomic
responses to technical and
biological perturbations
Rayna M. Harris
Neural Systems & Behavior Course
July 24, 2017
Technological advances now
allow single-cell transcriptomics
Lane K et at. (2017) Measuring Signaling and RNA-
Seq in the Same Cell Links Gene Expression to
Dynamic Patterns of NF-κB Activation. Cell Syst
Challenge: Brain tissues consists
of intricate neural layers & circuits
Brain Tissue
Single Neurons
Research Questions
• How does the process of cellular dissociation alter
gene expression?
• Does the process of cellular dissociation alter our
ability to identify biologically meaningful patterns of
gene expression?
Approach
Up-regulated genes
and pathways
Down-regulated genes
and pathways
Cembrowski et at. (2016) eLife
‘Tissue punch’ sample collection
Reproducible Bioinformatics
https://github.com/raynamharris/DissociationTest
Git for version control and GitHub
for sharing data and analysis
https://www.youtube.com/watch?v=taeAqimxXWo
The effect of cellular dissociation
on hippocampal transcriptomes
Harris RM et at. (2017) BioRxiv
The effect of a stressful experience
on hippocampal transcriptomes
Harris RM et at. (2017) BioRxiv
The effect of a cognitive training
on hippocampal transcriptomes
Harris RM et at. (2017) BioRxiv
Unique and shared responses to
technical and biological perturbations
Harris RM et at. (2017) BioRxiv
Meta analysis of reveals specific
and robust patterns of expression
Harris RM et at. (2017) BioRxiv
Summary
Thanks!
• Hans Hofmann & all the
Hofmann lab members
• UT Genomic Sequencing &
Analysis Facility
• UT Center for Computational
Biology & Bioinformatics
• Misha Matz & Rachel Wright
• Boris Zemelman, Laura Colgin
• Andre Fenton, Maddy Kao,
Ain Chung, Juan Marcos
Alarcon at NYU & SUNY
Downstate
• The Neural Systems &
Behavior Community
• Software/Data Carpentry
• NSF, NIH, Grass Foundation,
Promega, JAX Lab
15

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Hippocampal transcriptomic responses to technical and biological perturbations