A gene expression map of the mouse brain. Genepaint.org-A database of gene expression patterns.

Tens of thousands of novel genes have been identified by systematic DNA sequencing of a variety of genomes. Such gene sequences create a tremendous opportunity for addressing gene function by a variety of experimental approaches. To be attractive for genome-wide analysis, experimental strategies need not only to be efficient (high-throughput) but results also have to be systematized and made accessible in a way that they can be promptly leveraged by the scientific community. Having a genome-wide atlas of gene expression patterns with cellular resolution would be a rich resource to tackle a broad spectrum of biological and medical questions. The techniques to analyze gene expression have long been invented: mRNA in situ-hybridization (ISH) and antibody-based immunohistochemistry (IC). Traditionally, both ISH and IC are carried out on a gene-by-gene basis. Here we describe instrumentation (termed GenePaint) that permits automation of many aspects of ISH and image data acquisition. The throughput that is achieved renders investigations at a chromosome- or even genome-wide scale highly feasible. To effectively disseminate gene expression data, we have developed a database (www.gene-paint.org). Systematic annotation of gene expression data in reference to a standardized catalogue of anatomical structures makes it possible to compare expression patterns between specimens. For viewing expression patterns, GenePaint.org provides a “virtual microscope” which enables zooming and translocation of expression patterns. GenePaint is currently applied to large-scale studies of gene expression in the CNS of the mouse.