Skip to main content

Transforming the understanding
and treatment of mental illnesses.

Celebrating 75 Years! Learn More >>

Development of a BrainSpan RNA-seq Browser


Gregory Farber, Ph.D.
Office of Technology Development and Coordination


This initiative aims to create an RNA-seq web browser for the data contained in the BrainSpan Atlas, an NIMH-funded project that provides a comprehensive atlas of human brain development including high resolution images and RNA sequence data.


BrainSpan was designed to map gene expression patterns in the brain across time and space throughout the lifespan, using next-generation sequencing techniques. The range of ages represented in BrainSpan begins at 4 weeks post-conception and extends through approximately 40 years, encompassing 11 periods of development. The atlas comprises multiple data types, including high-resolution anatomical reference atlases based on both prenatal stages as well as from one adult stage. These atlases were created using high resolution imaging technology, as well as canonical brain cell staining methods. The BrainSpan team focused analysis on genes and brain regions matched to the genes and structures used in the NIH Blueprint-funded non-human primate atlas. Whole genome sequencing data are now available as well.

Although more than 50 papers have been published using the data in the BrainSpan Atlas, its use has nevertheless been limited to a small cadre of involved researchers. A straightforward web-browser is needed to enable the broader research community to mine the dataset. This initiative will create such a browser at modest cost. This web-based browser will allow a greater number of interested neuroscientists to query the valuable multi-modal data set and likely generate many hypothesis driven research proposals to study the neural underpinnings of mental health disorders, especially those with a developmental component.

Submit Comments