Decoding the Transcriptome of Neuronal Circuits

Paul J. Bonthuis, Christopher Gregg

Research output: Chapter in Book/Report/Conference proceedingChapter


Genomics is fostering broad discoveries across biological disciplines, including the neurosciences. However, the analysis of gene expression and gene regulation in the brain is complicated by the extraordinary cellular heterogeneity, complex connectivity, and dynamic physiology of the tissue. Indeed, one of the great challenges of modern neuroscience involves the functional and molecular classification of cells in the brain within the context of network connectivity. In parallel, a major area of focus in the field of genomics involves the development of technologies that can profile the transcriptome of single or small numbers of cells [38]. Thus, major objectives in these two fields are well aligned. Here, we review modern approaches for the analysis of gene expression at the cellular level in the brain. As detailed below, these new technologies involve both ex vivo genomics approaches and new and emerging technologies for in situ and in vivo imaging of molecules in the brain.
Original languageEnglish (US)
Title of host publicationNew Techniques in Systems Neuroscience
EditorsAdam D Douglass
StatePublished - Apr 14 2015
Externally publishedYes

Publication series

Name Biological and Medical Physics, Biomedical Engineering
ISSN (Print)1618-7210
ISSN (Electronic)2197-5647


  • reverse transcription primer
  • short read length
  • AgRP neuron
  • single cell RNAseq
  • terminal deoxynucleotide transferase


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