C57BL/6J mice used to construct the Allen Brain Atlas

The C57BL/6J (B6, 000664) mouse is helping scientists understand how the brain functions. The strain was used by the Allen Institute for Brain Science to construct the Allen Brain Atlas. The inaugural project of the Allen Institute, the Atlas is a free, publicly accessible, Web-based, three-dimensional map of the normal mouse brain. It pinpoints the location of over 21,000 mouse genes and shows the brain regions and cells where the genes are expressed during specific brain functions. Several thousand 25-micron thick (one sixth the thickness of a human hair) sections from the brains of 8-week old B6 males were probed to detect specific gene expression. Referred to as the "Google for gene activity in the brain," the Atlas is the most comprehensive resource available for examining gene activity at a cellular level in the brain. It contains more than 600 terabytes of data, enough to fill about 20,000 30-gigabyte iPods. The Atlas project has generated more than 85 million images of gene data and scans.

Because 90% of human genes have orthologs (counterparts) in the mouse, data in the atlas are expected to save valuable research time and lead to major advances in detecting, preventing, and treating brain diseases, such as Alzheimer's, Parkinson's, Lou Gehrig's and conditions such as autism. Atlas users merely have to click on a brain section to see which genes are active there. The Atlas is receiving considerable use: a Harvard researcher is using it to research treatments for obesity; a genomics research institute in Arizona used it to confirm its findings on short-term memory; a researcher at the Swedish Medical Center in Seattle hopes his work with the Brain Atlas will lead to new treatments for glioblastoma, a malignant form of brain cancer that kills about 17,000 Americans each year; and the U.S. Department of Defense commissioned the Allen Institute to study the effects of sleep deprivation on the brain.

Anyone can download the Atlas data, as long as they abide by the Allen Institute's terms of use and privacy policy, available online or by request. Users are asked to credit the Institute if its data are included in published work.

To find out more about the Allen Brain Atlas, visit the Web site, or read a transcript of a feature segment about the Brain Atlas aired on Public Television's News Hour with Jim Lehrer.


Lein E, Hawrylycz M, et al. 2007. Genome-wide atlas of gene expression in the adult mouse brain. Nature 445:168-76.

The Allen Institute Web site.