BrainStars: BrainStars API client for R

In BrainStars: query gene expression data and plots from BrainStars (B*)

Description

This R package can search and get gene expression data and plots from BrainStars (or B*, http://brainstars.org/).

Details

BrainStars 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 database has a REST API to query gene expression data and some kind of figures written by Dr. Takeya Kasukawa. This package is wrapper for BrainStars REST API in R. BrainStars data, images and texts (excluding ABA data and images) are licensed under a Creative Commons Attribution 2.1 Japan License.

References

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. (doi:10.1371/journal.pone.0023228) *equally contributed

BrainStars documentation built on Nov. 8, 2020, 5:58 p.m.