Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.

Mark S Cembrowski,Brenda C Shields,Lihua Wang,Ken Sugino,Nelson Spruston

doi:10.7554/elife.14997

Mark S Cembrowski, Brenda C Shields + Show 3 more

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https://doi.org/10.7554/elife.14997

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Journal: eLife	Publication Date: Apr 26, 2016
Citations: 366	License type: CC BY 4.0

Affiliation: Janelia Research Campus, Howard Hughes Medical Institute

Abstract

Clarifying gene expression in narrowly defined neuronal populations can provide insight into cellular identity, computation, and functionality. Here, we used next-generation RNA sequencing (RNA-seq) to produce a quantitative, whole genome characterization of gene expression for the major excitatory neuronal classes of the hippocampus; namely, granule cells and mossy cells of the dentate gyrus, and pyramidal cells of areas CA3, CA2, and CA1. Moreover, for the canonical cell classes of the trisynaptic loop, we profiled transcriptomes at both dorsal and ventral poles, producing a cell-class- and region-specific transcriptional description for these populations. This dataset clarifies the transcriptional properties and identities of lesser-known cell classes, and moreover reveals unexpected variation in the trisynaptic loop across the dorsal-ventral axis. We have created a public resource, Hipposeq (http://hipposeq.janelia.org), which provides analysis and visualization of these data and will act as a roadmap relating molecules to cells, circuits, and computation in the hippocampus.

Highlights

Gene expression profiling can be a powerful tool to understand the functionality and organization of cells and networks
Large-scale, quantitative gene expression profiling across neurons has typically been performed by microarray (Belgard et al, 2011; Siegert et al, 2012; Sugino et al, 2006), more recently the technically superior RNA sequencing (RNA-seq) (Shin et al, 2014) is finding application in the neurosciences (Cembrowski et al, 2016; Zeisel et al, 2015; Zhang et al, 2014)
The hippocampus is grossly comprised of five excitatory cell populations; namely, granule and mossy cells of the dentate gyrus (DG), and pyramidal cells of CA3, CA2, and CA1

Summary

Introduction

Gene expression profiling can be a powerful tool to understand the functionality and organization of cells and networks. Large-scale, quantitative gene expression profiling across neurons has typically been performed by microarray (Belgard et al, 2011; Siegert et al, 2012; Sugino et al, 2006), more recently the technically superior RNA-seq (Shin et al, 2014) is finding application in the neurosciences (Cembrowski et al, 2016; Zeisel et al, 2015; Zhang et al, 2014) Complementing these quantitative profiling methods is the mouse Allen Brain Atlas (ABA) (Lein et al, 2007), providing histological information from in situ hybridization (ISH) assays

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