Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis

Abstract

Event Abstract Back to Event Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis Yuko Okamura-Oho1, 2*, Masahiko Morita2, Kazuro Shimokawa3, Masaomi Nishimura2, Takehiro Tawara2 and Hideo Yokota2 1 Brain Research Network (BReNt), Japan 2 RIKEN, Japan 3 Tohoku University, Japan Microtomy techniques for tomographic acquisition of thin-sliced material sections and their block-face images, followed by high-throughput measurements of gene expression densities in the materials, enable ex-vivo transcriptomic analysis of intricate spatial expression patterns of wide varieties of RNA molecules in the whole anatomical context of any materials of interest, such as the brain and the embryos(ref 1). Using our microtomy technique, transcriptome tomography, we have created a database, ViBrism DB, in which measured expression densities are used for three dimensional (3D) expression map reconstruction and the maps can be superimposed on other voxel based images of the material (ref 2). Also the densities are directly used for co-expression analysis (ref 3). Here, we have launched a new platform of the DB for ex-vivo transcriptomic analysis of mouse developing brains on the web. The platform is equipped with a WEB-GL based 3D viewer of expression maps overlaid on the MRI images and anatomical region maps. Also co-expression network graphs of genes of interest are created and can be viewed with the expression maps. We will demonstrate integrated analysis of anatomical maps and topological co-expression graphs in the developing brains on this web-based platform. All users of the microtomy technique can use this platform to upload their own data sets on the DB and view their maps and networks on the website. Acknowledgements A part of this work was conducted within the Waxholm Space Task Force of the International Neuroinformatics Coordinating Facility (INCF) Program on Digital Brain Atlasing.