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The Journal of Neuroscience, May 1, 2003, 23(9):3607

Single-Cell Microarray Analysis in Hippocampus CA1: Demonstration and Validation of Cellular Heterogeneity

Fredrik Kamme¹, Ranelle Salunga², Jingxue Yu¹, Da-Thao Tran¹, Jessica Zhu¹, Lin Luo¹, Anton Bittner¹, Hong-Qing Guo¹, Nancy Miller³, Jackson Wan¹, and Mark Erlander²

¹ Johnson & Johnson Pharmaceutical Research and Development LLC, San Diego, California 92121, ² Arcturus Applied Genomics, Carlsbad, California 92008, and ³ OmniViz, Maynard, Massachusetts 01754

Laser capture microdissection in combination with microarrays allows for the expression analysis of thousands of genes in selected cells. Here we describe single-cell gene expression profiling of CA1 neurons in the rat hippocampus using a combination of laser capture, T7 RNA amplification, and cDNA microarray analysis. Subsequent cluster analysis of the microarray data identified two different cell types: pyramidal neurons and an interneuron. Cluster analysis also revealed differences among the pyramidal neurons, indicating that even a single cell type in vivo is not a homogeneous population of cells at the gene expression level. Microarray data were confirmed by quantitative RT-PCR and in situ hybridization. We also report on the reproducibility and sensitivity of this combination of methods. Single-cell gene expression profiling offers a powerful tool to tackle the complexity of the mammalian brain.

Key words: laser capture microdissection; gene expression profiling; RNA amplification; single cell; microarray; cell type definition

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Copyright © 2003 Society for Neuroscience  0270-6474/03/2393607-09$05.00/0

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