Skip to main content
Premium Trial:

Request an Annual Quote

Gene Expression For Allen Brain Atlas, First Step is 10% of Mouse Genome


As one of the least understood organs of the human body, the brain is a tantalizing puzzle for researchers investigating Alzheimer’s, Parkinson’s, and other diseases of the mind. And if you’re Paul Allen, Microsoft co-founder turned philanthropist and investor, maybe there’s something you can do to help. In fact, Allen chose the brain as the subject of his most recent investment in scientific research: the Allen Institute for Brain Science, founded in 2001.

The institute’s first major undertaking — the Allen Brain Atlas — began work in the summer of 2003 on an effort to comprehensively map gene expression in the mouse brain, and has now released the first results of its labors. In December, the Seattle-based institute made the first installment of its gene expression data available to researchers via the Internet — to the tune of 2,000 genes, or about 10 percent of the mouse genome.

Ultimately, the atlas will contain brain-localized gene expression data for about 24,000 mouse genes, says Ed Lein, the institute’s director of neuroscience, and may even sample from non-coding regions of the mouse genome as well. Like efforts to use transgenic mice to study where specific genes are expressed in the brain, the Allen Brain Atlas is attempting to be comprehensive in both the number of genes under investigation and where in the brain these genes are expressed, Lein says. Allan Jones, senior director for atlas operations for the institute, says he expects the project to be complete by the middle of 2006.

Project researchers are relying on in situ hybridization with digoxigenin-labeled probes to observe where individual genes are expressed in tissue sections taken at regular intervals from the brain of a standard laboratory mouse. The stained tissue sections are then photographed, and the image data uploaded to the institute’s website for display with an image browser. “We want to create an extension of people’s labs — akin to the way researchers use a national database,” says Jones.

Data access is open to all researchers — public or private sector — provided they sign the end-user license agreement. Among other stipulations, the agreement prohibits re-selling the data and requires permission from the institute to re-publish the data wholesale, Jones says, but doesn’t allow the institute to retain IP reach-through rights so long as the invention doesn’t prevent the institute from using the data itself.

— John S. MacNeil

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.