Multi-age Mouse Brain Mapping

Virtual brains at four post-natal age stages were made from real brains of C57BL/6J mice at 3 days, 7 days, 3 weeks and 8 weeks after birth (Table 1). Comprehensive gene expression densities of the whole brains were measured and 3D mapped with the TT method (3 (link)), as briefly described below. MR images and anatomical area maps of the 8-week-old brain were adopted from the WHS standard mouse image database (4 (link)); the images are downloadable from https://www.nitrc.org/projects/incfwhsmouse, and were used as the standard coordinates for the 8-week datasets. MR images at the other age stages were obtained by nuclear magnetic resonance (Bruker Bio Spin, AVANCE 400WB) at 9.4 Tesla at a spatial resolution of 100 μm and used as the coordinate space for each stage. ISH images, in which transcripts were histologically stained in 2D slices, were adopted from the BrainTx database (a mouse brain gene expression database http://www.cdtdb.neuroinf.jp/) (5 (link)), and transformed to the WHS coordinates system as described below.