title: A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain.
abstract: 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).
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Carol L
authors: CL
authors: Thompson
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Lydia
authors: L
authors: Ng
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Vilas
authors: V
authors: Menon
authors: 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.
authors: Salvador
authors: S
authors: Martinez
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Chang-Kyu
authors: CK
authors: Lee
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Katie
authors: K
authors: Glattfelder
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Susan M
authors: SM
authors: Sunkin
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Alex
authors: A
authors: Henry
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Christopher
authors: C
authors: Lau
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Chinh
authors: C
authors: Dang
authors: Instituto de Neurociencias UMH-CSIC, A03550 Alicante, Spain.
authors: Raquel
authors: R
authors: Garcia-Lopez
authors: Instituto de Neurociencias UMH-CSIC, A03550 Alicante, Spain.
authors: Almudena
authors: A
authors: Martinez-Ferre
authors: Instituto de Neurociencias UMH-CSIC, A03550 Alicante, Spain.
authors: Ana
authors: A
authors: Pombero
authors: Department of Psychiatry, Rock Hall, University of California at San Francisco, San Francisco, CA 94158, USA.
authors: John L R
authors: JLR
authors: Rubenstein
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Wayne B
authors: WB
authors: Wakeman
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: John
authors: J
authors: Hohmann
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Nick
authors: N
authors: Dee
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Andrew J
authors: AJ
authors: Sodt
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Rob
authors: R
authors: Young
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Kimberly
authors: K
authors: Smith
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Thuc-Nghi
authors: TN
authors: Nguyen
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Jolene
authors: J
authors: Kidney
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Leonard
authors: L
authors: Kuan
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Andreas
authors: A
authors: Jeromin
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Ajamete
authors: A
authors: Kaykas
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Jeremy
authors: J
authors: Miller
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Damon
authors: D
authors: Page
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Geri
authors: G
authors: Orta
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Amy
authors: A
authors: Bernard
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Zackery
authors: Z
authors: Riley
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Simon
authors: S
authors: Smith
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Paul
authors: P
authors: Wohnoutka
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA. Electronic address: mikeh@alleninstitute.org.
authors: Michael J
authors: MJ
authors: Hawrylycz
authors: Department of Human Anatomy and Psychobiology, University of Murcia, E30071 Murcia, Spain.
authors: Luis
authors: L
authors: Puelles
authors: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors: Allan R
authors: AR
authors: Jones
mesh_terms: D000818:Animals; D001921:Brain / Q000254:growth & development*; D001931:Brain Mapping / Q000379:methods*; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D051379:Mice