Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex

  • Nature Neurosciencevolume 21pages120129 (2018)
  • doi:10.1038/s41593-017-0029-5
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Activity-dependent transcriptional responses shape cortical function. However, a comprehensive understanding of the diversity of these responses across the full range of cortical cell types, and how these changes contribute to neuronal plasticity and disease, is lacking. To investigate the breadth of transcriptional changes that occur across cell types in the mouse visual cortex after exposure to light, we applied high-throughput single-cell RNA sequencing. We identified significant and divergent transcriptional responses to stimulation in each of the 30 cell types characterized, thus revealing 611 stimulus-responsive genes. Excitatory pyramidal neurons exhibited inter- and intralaminar heterogeneity in the induction of stimulus-responsive genes. Non-neuronal cells showed clear transcriptional responses that may regulate experience-dependent changes in neurovascular coupling and myelination. Together, these results reveal the dynamic landscape of the stimulus-dependent transcriptional changes occurring across cell types in the visual cortex; these changes are probably critical for cortical function and may be sites of deregulation in developmental brain disorders.

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We thank E. Griffith and J. Gray for critical reading of the manuscript; the HMS Single Cell Core for sample processing; and D. Harmin, A. Veres, D. Kotliar, H. Finucane, Y. Reshef, B. Hall, T. Otis, and D. Malhotra for discussions. This work was supported by funding from National Institutes of Health (NIH) grant R01 NS028829 and the ROADS Program funded by F. Hoffmann-La Roche Ltd. to M.E.G.; NIH grant R01 NS046579 to B.L.S.; the William F. Milton Fund to D.R.H.; NIH grant T32GM007753 to M.A.N.; NIH Training Grant in the Molecular Biology of Neurodegeneration 5T32AG000222-23 to S.H.; and a Burroughs Wellcome Fund Career award at the scientific interface, an Edward J. Mallinckrodt Scholarship, and NCI grant R33CA212697 to A.M.K.

Author information

Author notes

  1. Sinisa Hrvatin, Daniel R. Hochbaum and M. Aurel Nagy contributed equally to this work.


  1. Department of Neurobiology, Harvard Medical School, Boston, MA, USA

    • Sinisa Hrvatin
    • , M. Aurel Nagy
    • , Lucas Cheadle
    •  & Michael E. Greenberg
  2. Society of Fellows, Harvard University, Cambridge, MA, USA

    • Daniel R. Hochbaum
  3. Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA

    • Daniel R. Hochbaum
    • , Keiramarie Robertson
    •  & Bernardo L. Sabatini
  4. Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA

    • Marcelo Cicconet
  5. Department of Systems Biology, Harvard Medical School, Boston, MA, USA

    • Rapolas Zilionis
    •  & Allon M. Klein
  6. Vilnius University Institute of Biotechnology, Vilnius, Lithuania

    • Rapolas Zilionis
  7. ICCB-L Single Cell Core, Harvard Medical School, Boston, MA, USA

    • Alex Ratner
  8. Program for Bioinformatics and Integrative Genomics, Graduate School of Arts and Science, Division of Medical Sciences, Harvard University, Cambridge, MA, USA

    • Rebeca Borges-Monroy


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S.H., D.R.H., and M.A.N. conceived the study and designed all experiments. S.H. and D.R.H. developed the optimized dissociation protocol. S.H. and D.R.H. performed single-cell experiments with assistance from R.Z., A.M.K., and A.R. M.A.N. processed all sequencing data. S.H., M.A.N., and D.R.H. analyzed data with assistance from R.B.-M. and A.M.K. D.R.H., K.R., and L.C. carried out FISH experiments and imaging, D.R.H. analyzed the FISH data. M.C. and D.R.H. developed automated software for FISH analysis. S.H., D.R.H., M.A.N., and M.E.G. wrote the manuscript. M.E.G. and B.L.S. advised on all aspects of the study.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Bernardo L. Sabatini or Michael E. Greenberg.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–24

  2. Life Sciences Reporting Summary

  3. Supplementary Table 1

    GEO terms for genes induced by drug-cocktail treatment

  4. Supplementary Table 2

    Cell-type enriched genes

  5. Supplementary Table 3

    The 611 induced genes across cell types and time points

  6. Supplementary Table 4

    GEO terms for sensory-experience-regulated genes