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Transcriptional landscape of the prenatal human brain

Nature volume 508, pages 199206 (10 April 2014) | Download Citation


The anatomical and functional architecture of the human brain is mainly determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of the mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high-resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser-microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and post-mitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and outer subventricular zones even though the outer zone is expanded in humans. Both germinal and post-mitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in the frontal lobe. Finally, many neurodevelopmental disorder and human-evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development.

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We wish to thank the Allen Institute founders, P. G. Allen and J. Allen, for their vision, encouragement and support. We express our gratitude to past and present Allen Institute staff members R. Adams, A. Alpisa, A. Boe, E. Byrnes, M. Chapin, J. Chen, C. Copeland, N. Dotson, K. Fotheringham, E. Fulfs, M. Gasparrini, T. Gilbert, Z. Haradon, N. Hejazinia, N. Ivanov, J. Kinnunen, A. Kriedberg, J. Laoenkue, S. Levine, V. Menon, E. Mott, N. Motz, J. Pendergraft, L. Potekhina, J. Redmayne-Titley, D. Rosen, C. Simpson, S. Shi, L. Velasquez, U. Wagley, N. Wong and B. Youngstrom for their technical assistance. We would also like to thank J. Augustinack, T. Benner, A. Mayaram, M. Roy, A. van der Kouwe and L. Wald from the Fischl laboratory. Also, we wish to acknowledge Covance Genomics Laboratory (Seattle, Washington) for microarray probe generation, hybridization and scanning. In addition, we express our gratitude to Advanced Bioscience Resources, for providing tissue used for expression profiling and reference atlas generation as well as to the Laboratory of Developmental Biology, University of Washington, for providing tissue used for expression profiling and reference atlas generation. The Laboratory of Developmental Biology work was supported by the National Institutes of Health (NIH) Award Number 5R24HD0008836 from the Eunice Kennedy Shriver National Institute of Child Health & Human Development. The BrainSpan project was supported by Award Number RC2MH089921 (PIs: E. Lein and M. Hawrylycz, Allen Institute for Brain Science) from the National Institute of Mental Health. The content is solely the responsibility of the respective authors and does not necessarily represent the official views of the National Institute of Mental Health or the National Institutes of Health.

Author information

Author notes

    • Jeremy A. Miller
    •  & Song-Lin Ding

    These authors contributed equally to this work.


  1. Allen Institute for Brain Science, Seattle, Washington 98103, USA

    • Jeremy A. Miller
    • , Song-Lin Ding
    • , Susan M. Sunkin
    • , Kimberly A. Smith
    • , Lydia Ng
    • , Aaron Szafer
    • , Amanda Ebbert
    • , Zackery L. Riley
    • , Joshua J. Royall
    • , Kaylynn Aiona
    • , James M. Arnold
    • , Crissa Bennet
    • , Darren Bertagnolli
    • , Krissy Brouner
    • , Stephanie Butler
    • , Shiella Caldejon
    • , Anita Carey
    • , Christine Cuhaciyan
    • , Rachel A. Dalley
    • , Nick Dee
    • , Tim A. Dolbeare
    • , Benjamin A. C. Facer
    • , David Feng
    • , Tim P. Fliss
    • , Garrett Gee
    • , Jeff Goldy
    • , Lindsey Gourley
    • , Benjamin W. Gregor
    • , Guangyu Gu
    • , Robert E. Howard
    • , Jayson M. Jochim
    • , Chihchau L. Kuan
    • , Christopher Lau
    • , Chang-Kyu Lee
    • , Felix Lee
    • , Tracy A. Lemon
    • , Phil Lesnar
    • , Bergen McMurray
    • , Naveed Mastan
    • , Nerick Mosqueda
    • , Nhan-Kiet Ngo
    • , Julie Nyhus
    • , Aaron Oldre
    • , Eric Olson
    • , Jody Parente
    • , Patrick D. Parker
    • , Sheana E. Parry
    • , Melissa Reding
    • , Kate Roll
    • , David Sandman
    • , Melaine Sarreal
    • , Sheila Shapouri
    • , Nadiya V. Shapovalova
    • , Elaine H. Shen
    • , Nathan Sjoquist
    • , Clifford R. Slaughterbeck
    • , Michael Smith
    • , Andy J. Sodt
    • , Derric Williams
    • , Michael J. Hawrylycz
    • , Allan R. Jones
    • , John W. Phillips
    • , Paul Wohnoutka
    • , Chinh Dang
    • , Amy Bernard
    • , John G. Hohmann
    •  & Ed S. Lein
  2. Division of Genetic Medicine, Department of Pediatrics, University of Washington, 1959 North East Pacific Street, Box 356320, Seattle, Washington 98195, USA

    • Theresa Naluai-Cecchini
    •  & Ian A. Glass
  3. Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA

    • Allison Stevens
    • , Lilla Zöllei
    •  & Bruce Fischl
  4. Computer Science and AI Lab, MIT, Cambridge, Massachusetts 02139, USA

    • Allison Stevens
    •  & Bruce Fischl
  5. Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut 06510, USA

    • Mihovil Pletikos
    •  & Nenad Šestan
  6. Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA

    • Mark B. Gerstein
  7. Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA

    • Mark B. Gerstein
  8. Program in Neurogenetics, Department of Neurology and Semel Institute David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA

    • Daniel H. Geschwind
  9. Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington 98101, USA

    • Robert F. Hevner
  10. Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington 98105, USA

    • Robert F. Hevner
  11. Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA

    • Hao Huang
  12. Zilkha Neurogenetic Institute, and Department of Psychiatry, University of Southern California, Los Angeles, California 90033, USA

    • James A. Knowles
  13. Department of Pediatrics, Children’s Hospital, Los Angeles, California 90027, USA

    • Pat Levitt
  14. Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA

    • Pat Levitt


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E.S.L, S.-L.D., K.A.S. and S.M.S. contributed significantly to the overall project design. S.M.S, K.A.S., A.E., A.B., and P.W. managed the tissue and sample processing in the laboratory. K.A., J.M.A., C.B., D.B., K.B., S.B., S.C., A.C., C.C., R.A.D., G.Ge., J.G., L.G., B.W.G., R.E.H., T.A.L., Na.M., N.F.M., N.-K.N., A.O., E.O., J.Pa., P.D.P., S.E.P., M.P., Me.R., J.J.R., K.R., D.S., Me.S., S.S., N.V.S. and Mi.S. contributed to tissue and sample processing. E.H.S., Z.L.R., T.N.-C., and I.A.G. contributed to establishing the tissue acquisition pipeline. N.D., J.N. and A.B. contributed to protocol development. A.S.P., L.Z., B.F., and H.H. contributed to MR and DWI imaging and analysis. J.M.J., C.R.S., and D.W. provided engineering support. S.-L.D., R.A.D., P.D.P., D.S. and J.G.H. contributed to the neuroanatomical design and implementation. S.-L.D., B.A.C.F., Ph.L., B.M., J.J.R., R.F.H., N.Se. and J.G.H. contributed to the reference atlas design, quality control and implementation. L.N., A.S. and C.D. managed the creation of the data pipeline, visualization and mining tools. L.N., A.S., T.A.D., D.F., T.P.F., G.Gu, C.L.K., C.La., F.L., N.Sj. and A.J.S. contributed to the creation of the data pipeline, visualization and mining tools. J.A.M., S.-L.D., R.F.H., C.-K.L., M.J.H., S.M.S. and E.S.L. contributed to data analysis and interpretation. M.B.G., D.H.G., J.A.K., Pa.L., J.W.P., N.Se. and A.R.J. contributed to overall project design and consortium management. E.S.L. and M.J.H. conceived the project, and the manuscript was written by J.A.M. and E.S.L. with input from all other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Ed S. Lein.

These data are freely accessible as part of the BrainSpan Atlas of the Developing Human Brain (, also available via the Allen Brain Atlas data portal (

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Methods and Supplementary Table 1, which gives additional biological insights into the prenatal human brain.

Excel files

  1. 1.

    Supplementary Table 2

    Complete ontology for the BrainSpan project, showing the subset of structures and layers assayed in this study. Further details in the "Key" tab of the spreadsheet.

  2. 2.

    Supplementary Table 3 and 4

    Layer of maximal expression (with statistics) for each gene in each brain (Supplementary Table 3). These data were used for Figure 2d. Enrichment analysis for laminar genes at 21pcw (Supplementary Table 4). Significantly enriched gene ontology and brain-related categories are listed. Further details in the "Key" tab of the spreadsheet.

  3. 3.

    Supplementary Table 5

    Module assignments and module membership for each gene in the cortical network. Genes listed in Figure 3b were chosen from this table. Further details in the "Key" tab of the spreadsheet.

  4. 4.

    Supplementary Table 6

    Enrichment analysis for genes in each cortical network module. Significantly enriched DAVID categories and relevant brain-related categories, including cell type enrichment are listed. Details are described in the worksheet labeled "Key".

  5. 5.

    Supplementary Table 7

    Enrichment analysis for genes in each germinal network module. Significantly enriched DAVID categories and relevant brain-related categories, including cell type enrichment are listed. Details are described in the worksheet labeled "Key".

  6. 6.

    Supplementary Table 8

    150 marker genes for human and/or mouse subplate, along with evidence for defining these genes as SP markers. Genes listed in Figure 4 were selected from this table. Further details in the "Key" tab of the spreadsheet.

  7. 7.

    Supplementary Table 9

    All genes identified as showing frontal to temporal gradient patterning in the developing human neocortex are included. Subsets of these genes, which are associated with human accelerated conserved noncoding sequences (haCNSs) or that are consistent with mouse, are also highlighted. Further details in the "Key" tab of the spreadsheet.

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