A Digital Atlas of Ion Channels Expression Patterns in the Two-Week-Old Rat Brain

Numerous studies exist showing expression of ion channels in various species, stages, and planes of sectioning. However, it is difficult to directly compare levels and sites of expression of all channels (channelome) using this published data alone. Our aim is to put all this information into a common reference frame. This task requires a redetermination of expression patterns for the channelome in a particular species and stage, a systematic quantification of expression strength, and a method to place this information into a digital, searchable atlas. Once constructed, such an atlas would allow one to compare and contrast the expression patterns of hundreds of channels.

The Allen Brain Atlas [1] provides a first important step towards the goal of standardization. It contains the expression patterns of ~300 ion channels in serial sections through the adult mouse brain. We have developed highly reproducible methods of brain orientation so that data obtained from different specimens can be used for comparative analysis. Moreover, we have re-determined the expression patterns of nearly all ion channels in the two-week-old rat brain, a specimen frequently used for electrophysiological studies. Furthermore, we used a previously developed atlasing method (subdivision meshes) to faithfully model the shape of the various brain regions [2] and quantified gene expression strength [3], following a previously established procedure (http://www.geneatlas.org).

We illustrate our approach using inwardly rectifying potassium channels (Kir) and show some of the quantitative comparisons of the expression patterns and strengths to emphasize the usefulness of this new digital atlas.

References:
1. Lein, E.S., et al., Genome-wide atlas of gene expression in the adult mouse brain. Nature, 2007. 445(7124): p. 168-76.
2. Carson, J.P., et al., A digital atlas to characterize the mouse brain transcriptome. PLoS Comput Biol, 2005. 1(4): p. e41.
3. Carson, J.P., G. Eichele, and W. Chiu, A method for automated detection of gene expression required for the establishment of a digital transcriptome-wide gene expression atlas. J Microsc, 2005. 217(Pt 3): p. 275-81.