1. Hippocampal transcriptomic
responses to technical and
biological perturbations
Rayna M. Harris
Neural Systems & Behavior Course
July 24, 2017

2. 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

3. Challenge: Brain tissues consists
of intricate neural layers & circuits
Brain Tissue
Single Neurons

4. 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?

5. Approach
Up-regulated genes
and pathways
Down-regulated genes
and pathways
Cembrowski et at. (2016) eLife

6. ‘Tissue punch’ sample collection

7. Reproducible Bioinformatics
https://github.com/raynamharris/DissociationTest

8. Git for version control and GitHub
for sharing data and analysis
https://www.youtube.com/watch?v=taeAqimxXWo

9. The effect of cellular dissociation
on hippocampal transcriptomes
Harris RM et at. (2017) BioRxiv

10. The effect of a stressful experience
on hippocampal transcriptomes
Harris RM et at. (2017) BioRxiv

11. The effect of a cognitive training
on hippocampal transcriptomes
Harris RM et at. (2017) BioRxiv

12. Unique and shared responses to
technical and biological perturbations
Harris RM et at. (2017) BioRxiv

13. Meta analysis of reveals specific
and robust patterns of expression
Harris RM et at. (2017) BioRxiv

14. Summary

15. 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
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