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mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex

Nature Neuroscience volume 16, pages 499506 (2013) | Download Citation

Abstract

The complexity of the adult brain is a result of both developmental processes and experience-dependent circuit formation. One way to look at the differences between embryonic and adult brain is to examine gene expression. Previous studies have used microarrays to address this in a global manner. However, the transcriptome is more complex than gene expression levels alone, as alternative splicing and RNA editing generate a diverse set of mature transcripts. Here we report a high-resolution transcriptome data set of mouse cerebral cortex at embryonic and adult stages using RNA sequencing (RNA-Seq). We found many differences in gene expression, splicing and RNA editing between embryonic and adult cerebral cortex. Each data set was validated technically and biologically, and in each case we found our RNA-Seq observations to have predictive validity. We provide this data set and analysis as a resource for understanding gene expression in the embryonic and adult cerebral cortex.

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Gene Expression Omnibus

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NCBI Reference Sequence

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Acknowledgements

The authors would like to thank E. Lindquist for excellent technical assistance. We would also like to thank M. Do for assistance with cloning experiments. This research was supported in part by the Intramural Research Program of the US National Institutes of Health, National Institute on Aging (project AG000947) and by the Swedish Research Council and Swedish Brain Power.

Author information

Affiliations

  1. Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.

    • Allissa A Dillman
    • , David N Hauser
    • , Melissa K McCoy
    • , Iakov N Rudenko
    •  & Mark R Cookson
  2. Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.

    • Allissa A Dillman
    •  & Dagmar Galter
  3. Brown University/National Institutes of Health Graduate Partnership Program, Department of Neuroscience, Brown University, Providence, Rhode Island, USA.

    • David N Hauser
  4. Computational Biology Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.

    • J Raphael Gibbs
  5. Reta Lila Weston Laboratories and Department of Molecular Neuroscience, University College London Institute of Neurology, London, UK.

    • J Raphael Gibbs
  6. Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.

    • Michael A Nalls

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Contributions

A.A.D. performed the RNA-Seq experiments and analyzed the data. J.R.G. and M.A.N. provided additional analytical approaches. D.N.H., M.K.M. and I.N.R. performed mouse dissections and contributed additional validation results. M.R.C. and D.G. supervised the project. M.R.C. and A.A.D. wrote the paper with contributions from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Mark R Cookson.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–13, Supplementary Tables 1 and 5–7

Excel files

  1. 1.

    Supplementary Table 2

    Gene expression in the embryonic and adult mouse cerebral cortex. (CSV format)

  2. 2.

    Supplementary Table 3

    Alternate exon usage in the embryonic and adult mouse cerebral cortex. (CSV format)

  3. 3.

    Supplementary Table 4

    Adenosine-to-inosine RNA editing in the embryonic and adult mouse cerebral cortex. (CSV format)

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DOI

https://doi.org/10.1038/nn.3332

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