A High-Resolution Spatiotemporal Atlas of Gene Expression of the Developing Mouse Brain

Highlights

• We generated a survey ∼2,100 genes over seven stages of mouse brain development

• Automated and manual image analysis allows discovery of genoarchitecture

• Transcription factors exhibit temporal shifts in molecular organizing principles

• A transcription factor code of 83 genes uniquely identifies age and brain region

Summary

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for ∼2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).