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Hippocampal transcriptomic responses to technical and biological perturbations

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Hippocampal transcriptomic responses to technical and biological perturbations

  1. 1. Hippocampal transcriptomic responses to technical and biological perturbations Rayna M. Harris Neural Systems & Behavior Course July 24, 2017
  2. 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. 3. Challenge: Brain tissues consists of intricate neural layers & circuits Brain Tissue Single Neurons
  4. 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. 5. Approach Up-regulated genes and pathways Down-regulated genes and pathways Cembrowski et at. (2016) eLife
  6. 6. ‘Tissue punch’ sample collection
  7. 7. Reproducible Bioinformatics https://github.com/raynamharris/DissociationTest
  8. 8. Git for version control and GitHub for sharing data and analysis https://www.youtube.com/watch?v=taeAqimxXWo
  9. 9. The effect of cellular dissociation on hippocampal transcriptomes Harris RM et at. (2017) BioRxiv
  10. 10. The effect of a stressful experience on hippocampal transcriptomes Harris RM et at. (2017) BioRxiv
  11. 11. The effect of a cognitive training on hippocampal transcriptomes Harris RM et at. (2017) BioRxiv
  12. 12. Unique and shared responses to technical and biological perturbations Harris RM et at. (2017) BioRxiv
  13. 13. Meta analysis of reveals specific and robust patterns of expression Harris RM et at. (2017) BioRxiv
  14. 14. Summary
  15. 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 15

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