The gene expression data used for this atlas is based on microarray and RNA sequencing studies and publicly available in situ hybridization images in early embryonic, late embryonic, early postnatal and adult mice. Read more here and see Hoerder-Suabedissen et al., 2012.
A visualization of genes with a specific or enriched expression in the mouse subplate, including data from early embryonic to adult stages.
The Subplate Gene Expression Atlas illustrates the cortical expression patterns of 426 selected genes. These genes were identified by both microarray/RNA seq and in situ hybridization studies as preferentially expressed in subplate at at least one developmental age (E15, E18, P4/P7/P8 and Adult). The expression patterns illustrated in the Atlas are derived from published or publicly available in situ hybridization images (see below). Expression levels were categorized for the illustration according to two criteria: abundance of cells (abundant vs sparse) and expression level (no labeling detected vs weak labeling vs strong labeling). It is important to note that expression levels are purely qualitative and should neither be compared between ages nor between different genes.
A microarray based approach was used to identify genes expressed at a higher level in the mouse subplate compared to overlying cortical plate at embryonic ages E15.5 and E18.5 and subplate compared to overlying layer 6a at postnatal P8 (Affymetrix Gene ST1.0 at E15, Affymetrix 430 2.0 for E18.5 and P8). Data was RMA normalized and putatively differential gene expression (>1.5-fold higher in subplate, nominal p<0.05) determined. High-throughput sequencing data was used to identify genes expressed at a higher level (>1.5 fold) in the adult mouse subplate/layer 6b compared to the adjacent layer 6a. In total, 1642 genes were identified as potentially SP enriched at least at one age. Of these, 426 genes could be confirmed as SP enriched using published or publicly available databases including Allen Mouse Brain Atlas (Adult), Allen Developing Mouse Brain Atlas (E15.5, E18.5, P4 and P14), Genepaint.org (E14.5, P7 and Adult) and or our own in situ hybridization or immunohistochemistry experiments. The schematic results of this are presented here in the “Subplate Gene Expression Atlas”. Genes with uniform or no labelling, or for which no images could be found, were not included.
Using the above approach, we selected against genes that are subplate expressed, but are additionally expressed in layer 6a at equal or higher levels. Furthermore, there may be subplate specific or enriched genes not identified by the microarrays. Thus, genes important for the differentiation of the deep cortical layers or those relevant in the specification of subplate prior to E15.5 may not be included here.
This Subplate Gene Expression Atlas is an ongoing project and over time more genes identified by other sources may be added if there is convincing evidence of their subplate enriched expression at the above time points.
More details on the data used for this Atlas can be found in the following papers:
Anna Hoerder-Suabedissen, Franziska M Oeschger, Michelle L Krishnan, T Grant Belgard, Wei Zhi Wang, Sheena Lee, Caleb Webber, Enrico G Petretto, A David Edwards, Zoltán Molnár (2012) Expression Profiling of Mouse Subplate Reveals a Spatially and Temporally Dynamic Gene Network and Disease Association with Autism and Schizophrenia (In press)
Franziska M. Oeschger, Wei-Zhi Wang, Sheena Lee, Fernando García-Moreno, André M. Goffinet, Maria L. Arbonés, Sonja Rakic and Zoltán Molnár Gene Expression Analysis of the Embryonic Subplate Cereb. Cortex (2011)
T. Grant Belgard, Ana C. Marques, Peter L. Oliver, Hatice Ozel Abaan, Tamara M. Sirey, Anna Hoerder-Suabedissen, Fernando García-Moreno, Zoltán Molnár, Elliott H. Margulies, Chris P. Ponting A Transcriptomic Atlas of Mouse Neocortical Layers Neuron, Volume 71, Issue 4, 605-616, 25 August 2011
Anna Hoerder-Suabedissen, Wei Zhi Wang, Sheena Lee, Kay E. Davies, André M. Goffinet, Sonja Rakić, John Parnavelas, Kerstin Reim, Margareta Nicolić, Ole Paulsen, and Zoltán Molnár Novel Markers Reveal Subpopulations of Subplate Neurons in the Murine Cerebral Cortex Cereb. Cortex (2009) 19(8): 1738-1750
Lydia Ng, Amy Bernard, Chris Lau, Caroline C Overly, Hong-Wei Dong, Chihchau Kuan, Sayan Pathak, Susan M Sunkin, Chinh Dang, Jason W Bohland, Hemant Bokil, Partha P Mitra, Luis Puelles, John Hohmann, David J Anderson, Ed S Lein, Allan R Jones & Michael Hawrylycz An anatomic gene expression atlas of the adult mouse brain Nature Neuroscience 12, 356 - 362 (2009)
We would be happy to hear if you reference the Subplate Atlas in your publication.
Anna Hoerder-Suabedissen
Zoltán Molnár MD DPhil
Professor of Developmental Neurobiology
Cerebral cortical development
Department of Physiology, Anatomy and Genetics
Oxford University
Franziska Oeschger DPhil
Oleg Lavrovsky
The Subplate Gene Expression Atlas is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Copyright © 2012 Anna Hoerder-Suabedissen, Franziska Oeschger, Oleg Lavrovsky. Source code available.
The Allen Institute for Brain Science (logo and words), Allen Brain Atlas, Allen, Brain Explorer and Fueling Discovery are registered trademarks of the Allen Institute.
Terms of Ownership, Liability and Use of the University of Oxford apply.