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Neuron. 2014 Jul 16;83(2):309-323. doi: 10.1016/j.neuron.2014.05.033. Epub 2014 Jun 19.

A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain.

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Allen Institute for Brain Science, Seattle, WA 98103, USA.
Instituto de Neurociencias UMH-CSIC, A03550 Alicante, Spain; Centro de Investigacion Biomedica en Red de Salud Mental (CIBERSAM) and IMIB-Arrixaca of Instituto de Salud Carlos III, 30120 Murcia, Spain.
Instituto de Neurociencias UMH-CSIC, A03550 Alicante, Spain.
Department of Psychiatry, Rock Hall, University of California at San Francisco, San Francisco, CA 94158, USA.
Allen Institute for Brain Science, Seattle, WA 98103, USA. Electronic address:
Department of Human Anatomy and Psychobiology, University of Murcia, E30071 Murcia, Spain.


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 (

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