BrainStars (B*)


About the BrainStars database

About BrainStars

BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions.

For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2).

These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database.


BrainStars data was derived by members in Functional Genomics Unit, Laboratory for Systems Biology, and Laboratory for Neocortical Development, RIKEN Center for Developmental Biology (CDB), and in Department of Anatomy and Neurobiology, Kinki University School of Medicine.

The ViBrism cross-section images and a 3-D brain model were provided by Yuko Okamura-Oho, Masaomi Nishimura and Hideo Yokota in Living Matter Simulation Research Group, Advanced Computational Sciences Department, RIKEN Advanced Science Institute (ASI) and Bio-research Infrastructure Construction Team, VCAD System Research Program, RIKEN Center for Intellectual Property Strategies (CIPS).

The Allen Brain Atlas cross-section images were downloaded from the site for Allen Mouse Brain Atals, Seattle (WA), Allen Institute for Brain Science. © 2008.


When you refer the database, please cite the following paper:

Takeya Kasukawa*, Koh-hei Masumoto*, Itoshi Nikaido*, Mamoru Nagano, Kenichiro D. Uno, Kaori Tsujino, Carina Hanashima, Yasufumi Shigeyoshi, and Hiroki R. Ueda: Quantitative Expression Profile of Distinct Functional Regions in the Adult Mouse Brain, PLoS ONE 6(8), e23228, 2011. (Journal page) ( doi:10.1371/journal.pone.0023228) *equally contributed


BrainStars data, images and texts (excluding ABA data and images) are licensed under a Creative Commons Attribution 2.1 Japan License.
Creative Commons License


This work was done as a part of the Genome Network Project from the Ministry of Education, Culture, Sports, Science and Technology of Japan.


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Copyright © 2009 RIKEN Center for developmental Biology.