Genome-wide atlas of gene expression in the adult mouse brain (original) (raw)

References

  1. Zapala, M. A. et al. Adult mouse brain gene expression patterns bear an embryologic imprint. Proc. Natl Acad. Sci. USA 102, 10357–10362 (2005)
    Article ADS CAS Google Scholar
  2. Datson, N. A., van der Perk, J., de Kloet, E. R. & Vreugdenhil, E. Expression profile of 30,000 genes in rat hippocampus using SAGE. Hippocampus 11, 430–444 (2001)
    Article CAS Google Scholar
  3. Sandberg, R. et al. Regional and strain-specific gene expression mapping in the adult mouse brain. Proc. Natl Acad. Sci. USA 97, 11038–11043 (2000)
    Article ADS CAS Google Scholar
  4. Siddiqui, A. S. et al. A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc. Natl Acad. Sci. USA 102, 18485–18490 (2005)
    Article ADS CAS Google Scholar
  5. Kamme, F. et al. Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity. J. Neurosci. 23, 3607–3615 (2003)
    Article CAS Google Scholar
  6. Sugino, K. et al. Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nature Neurosci. 9, 99–107 (2006)
    Article CAS Google Scholar
  7. Markram, H. et al. Interneurons of the neocortical inhibitory system. Nature Rev. Neurosci. 5, 793–807 (2004)
    Article CAS Google Scholar
  8. Toledo-Rodriguez, M., Goodman, P., Illic, M., Wu, C. & Markram, H. Neuropeptide and calcium-binding protein gene expression profiles predict neuronal anatomical type in the juvenile rat. J. Physiol. (Lond.) 567, 401–413 (2005)
    Article CAS Google Scholar
  9. Monyer, H. & Markram, H. Interneuron diversity series: Molecular and genetic tools to study GABAergic interneuron diversity and function. Trends Neurosci. 27, 90–97 (2004)
    Article CAS Google Scholar
  10. Christiansen, J. H. et al. EMAGE: a spatial database of gene expression patterns during mouse embryo development. Nucleic Acids Res. 34, D637–D641 (2006)
    Article CAS Google Scholar
  11. Gong, S. et al. A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature 425, 917–925 (2003)
    Article ADS CAS Google Scholar
  12. Visel, A., Thaller, C. & Eichele, G. GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res. 32, D552–D556 (2004)
    Article CAS Google Scholar
  13. Gray, P. A. et al. Mouse brain organization revealed through direct genome-scale TF expression analysis. Science 306, 2255–2257 (2004)
    Article ADS CAS Google Scholar
  14. Magdaleno, S. et al. BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. PLoS Biol. 4, e86 (2006)
    Article Google Scholar
  15. Boguski, M. S. & Jones, A. R. Neurogenomics: at the intersection of neurobiology and genome sciences. Nature Neurosci. 7, 429–433 (2004)
    Article CAS Google Scholar
  16. Dennis, G. et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, P3 (2003)
    Article Google Scholar
  17. Kirkwood, A., Rioult, M. C. & Bear, M. F. Experience-dependent modification of synaptic plasticity in visual cortex. Nature 381, 526–528 (1996)
    Article ADS CAS Google Scholar
  18. Elias, C. F. et al. Characterization of CART neurons in the rat and human hypothalamus. J. Comp. Neurol. 432, 1–19 (2001)
    Article CAS Google Scholar
  19. Heuer, H. et al. Connective tissue growth factor: a novel marker of layer VII neurons in the rat cerebral cortex. Neuroscience 119, 43–52 (2003)
    Article CAS Google Scholar
  20. Zola-Morgan, S., Squire, L. R. & Amaral, D. G. Human amnesia and the medial temporal region: enduring memory impairment following a bilateral lesion limited to field CA1 of the hippocampus. J. Neurosci. 6, 2950–2967 (1986)
    Article CAS Google Scholar
  21. Scoville, W. B. & Milner, B. Loss of recent memory after bilateral hippocampal lesions. 1957. J. Neuropsychiatry Clin. Neurosci. 12, 103–113 (2000)
    Article CAS Google Scholar
  22. Lorente de Nó, R. Studies on the structure of the cerebral cortex. II. Continuation of the study of the ammonic system. J. Psychol. Neurol. (Lpz.) 46, 113–177 (1934)
    Google Scholar
  23. Amaral, D. G. & Witter, M. P. The three-dimensional organization of the hippocampal formation: a review of anatomical data. Neuroscience 31, 571–591 (1989)
    Article CAS Google Scholar
  24. Ishizuka, N., Weber, J. & Amaral, D. G. Organization of intrahippocampal projections originating from CA3 pyramidal cells in the rat. J. Comp. Neurol. 295, 580–623 (1990)
    Article CAS Google Scholar
  25. Tole, S., Christian, C. & Grove, E. A. Early specification and autonomous development of cortical fields in the mouse hippocampus. Development 124, 4959–4970 (1997)
    CAS Google Scholar
  26. Lein, E. S., Zhao, X. & Gage, F. H. Defining a molecular atlas of the hippocampus using DNA microarrays and high-throughput in situ hybridization. J. Neurosci. 24, 3879–3889 (2004)
    Article CAS Google Scholar
  27. Yamagata, M., Sanes, J. R. & Weiner, J. A. Synaptic adhesion molecules. Curr. Opin. Cell Biol. 15, 621–632 (2003)
    Article CAS Google Scholar
  28. Small, S. A. The longitudinal axis of the hippocampal formation: its anatomy, circuitry, and role in cognitive function. Rev. Neurosci. 13, 183–194 (2002)
    Article Google Scholar
  29. Moser, M. B. & Moser, E. I. Functional differentiation in the hippocampus. Hippocampus 8, 608–619 (1998)
    Article CAS Google Scholar
  30. Bannerman, D. M. et al. Regional dissociations within the hippocampus—memory and anxiety. Neurosci. Biobehav. Rev. 28, 273–283 (2004)
    Article CAS Google Scholar
  31. Voogd, J., Hess, D. & Marani, E. The Parasagittal Zonation of the Cerebellar Cortex in Cat and Monkey: Topography, Distribution of Acetylcholinesterase, and Development (ed. King, E. S.) (Liss, New York, 1987)
    Google Scholar
  32. Herrup, K. & Kuemerle, B. The compartmentalization of the cerebellum. Annu. Rev. Neurosci. 20, 61–90 (1997)
    Article CAS Google Scholar
  33. Hawkes, R. & Herrup, K. Aldolase C/zebrin II and the regionalization of the cerebellum. J. Mol. Neurosci. 6, 147–158 (1995)
    Article CAS Google Scholar
  34. Gravel, C. & Hawkes, R. Parasagittal organization of the rat cerebellar cortex: direct comparison of Purkinje cell compartments and the organization of the spinocerebellar projection. J. Comp. Neurol. 291, 79–102 (1990)
    Article CAS Google Scholar
  35. Blackshaw, S. & Snyder, S. H. Encephalopsin: a novel mammalian extraretinal opsin discretely localized in the brain. J. Neurosci. 19, 3681–3690 (1999)
    Article CAS Google Scholar
  36. Eberwine, J., Belt, B., Kacharmina, J. E. & Miyashiro, K. Analysis of subcellularly localized mRNAs using in situ hybridization, mRNA amplification, and expression profiling. Neurochem. Res. 27, 1065–1077 (2002)
    Article CAS Google Scholar
  37. Kang, H. & Schuman, E. M. A requirement for local protein synthesis in neurotrophin-induced hippocampal synaptic plasticity. Science 273, 1402–1406 (1996)
    Article ADS CAS Google Scholar
  38. Huber, K. M., Kayser, M. S. & Bear, M. F. Role for rapid dendritic protein synthesis in hippocampal mGluR-dependent long-term depression. Science 288, 1254–1257 (2000)
    Article ADS CAS Google Scholar
  39. Burgin, K. E. et al. In situ hybridization histochemistry of Ca2+/calmodulin-dependent protein kinase in developing rat brain. J. Neurosci. 10, 1788–1798 (1990)
    Article CAS Google Scholar
  40. Trapp, B. D. et al. Spatial segregation of mRNA encoding myelin-specific proteins. Proc. Natl Acad. Sci. USA 84, 7773–7777 (1987)
    Article ADS CAS Google Scholar
  41. Kindler, S., Wang, H., Richter, D. & Tiedge, H. RNA transport and local control of translation. Annu. Rev. Cell Dev. Biol. 21, 223–245 (2005)
    Article CAS Google Scholar
  42. Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005)
    Article ADS CAS Google Scholar
  43. Panda, S. et al. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109, 307–320 (2002)
    Article CAS Google Scholar
  44. Vavouri, T. & Elgar, G. Prediction of cis-regulatory elements using binding site matrices—the successes, the failures and the reasons for both. Curr. Opin. Genet. Dev. 15, 395–402 (2005)
    Article CAS Google Scholar
  45. Luquet, S., Perez, F. A., Hnasko, T. S. & Palmiter, R. D. NPY/AgRP neurons are essential for feeding in adult mice but can be ablated in neonates. Science 310, 683–685 (2005)
    Article ADS CAS Google Scholar
  46. Lechner, H. A., Lein, E. S. & Callaway, E. M. A genetic method for selective and quickly reversible silencing of Mammalian neurons. J. Neurosci. 22, 5287–5290 (2002)
    Article CAS Google Scholar
  47. Yoshihara, Y. et al. A genetic approach to visualization of multisynaptic neural pathways using plant lectin transgene. Neuron 22, 33–41 (1999)
    Article CAS Google Scholar
  48. DeFalco, J. et al. Virus-assisted mapping of neural inputs to a feeding center in the hypothalamus. Science 291, 2608–2613 (2001)
    Article ADS CAS Google Scholar
  49. Brecht, M. et al. Novel approaches to monitor and manipulate single neurons in vivo. J. Neurosci. 24, 9223–9227 (2004)
    Article CAS Google Scholar
  50. Ng, L. et al. Neuroinformatics for genome-wide 3-D gene expression mapping in the mouse brain. IEEE Trans. Comput. Biol. Bioinform. (in the press).
  51. Thompson, P. M. & Toga, A. W. in Handbook of Medical Imaging: Processing and Analysis (ed. Bankman, I. N.) (Academic Press, San Diego, 2000)
    Google Scholar
  52. Viola, P. & Wells, W. M. Alignment by maximization of mutual information. Int. J. Comput. Vis. 24, 137–154 (1997)
    Article Google Scholar
  53. Chan, T. F. & Shen, J. Image Processing and Analysis: Variation, PDE, Wavelet, and Stochastic Methods (Society for Industrial and Applied Mathematics, Philadelphia, 2005)
    Book Google Scholar
  54. Lein, E. S., Callaway, E. M., Albright, T. D. & Gage, F. H. Redefining the boundaries of the hippocampal CA2 subfield in the mouse using gene expression and 3-dimensional reconstruction. J. Comp. Neurol. 485, 1–10 (2005)
    Article CAS Google Scholar
  55. Swanson, L. W. Brain Maps: Structure of the Rat Brain (Elsevier, Amsterdam, 2004)
    Google Scholar

Download references

Acknowledgements

This work was sponsored by the Allen Institute for Brain Science. The authors wish to thank the Allen Institute founders, P. G. Allen and J. Patton, for their vision, encouragement and support. We also wish to thank key Institute advisors, K. Dooley and S. Coliton, as well as the Scientific Advisory Board for the Atlas project, M. Tessier-Lavigne, D. Anderson, C. Dulac, R. Gibbs, S. Paul, G. Schuler, A. W. Toga and J. Takahashi, for their scientific guidance and dedication to the successful execution of the Atlas project. We would particularly like to acknowledge D. Anderson for his role in the conceptual genesis and continual refinement of Atlas goals, as well as M. Tessier-Lavigne for key scientific and organizational leadership throughout the project. We also thank C. Jennings for his critical reading of the manuscript.

Author Contributions Neuroscience Group: E.S.L. (group leader), A.B., L.C., M.P.H., M.T.M, C.L.T., T.A.Z. Informatics Group: M.J.H. (group leader), C.L.K., C.L., L.L.N., S.D.P. Production Groups: Allen Institute for Brain Science: P.E.W. (group leader), S.M.S. (group leader), R.A.J. (group leader), M.A., A.F.B., E.J.B., S.D., N.R.D., A.L.D., T.D., E.D., M.J.D., J.G.D., A.J.E., L.K.E., S.R.F., S.N.G., K.J.G., K.R.H., M.R.H., J.M.K., R.H.K., J.H.L., T.A.L., L.T.L., R.J.M., N.F.M., R.N., G.J.O., T.H.P., S.E.P., O.C.P., R.B.P., Z.L.R., H.R.R., S.A.R., J.J.R., N.R.S., K.S., N.V.S., T.S., C.R.S., S.C.S., K.A.S., N.N.S., K.-R.S., L.R.V., R.M.W., C.K.W., V.Y.W., X.F.Y.; Baylor College of Medicine: C.T. (group leader), N.A., L.C. (Li Chen), T.-M.C., A.C., R.F., A.J.L., Y.L., M.J.R., A.T., M.W., M.B.Y., B.Z.; Max Planck Institute: G.E. (group leader), A.V. Technology Group: C.N.D. (group leader), C.D.T. (group leader), A.B. (Amy Bensinger), K.S.B., M.C.C., J.C., B.E.C., T.A.D., B.J.D., T.P.F., C.F. (Cliff Frensley), D.P.J., P.T.K., R.K., A.R.L., K.D.L., J.M., B.I.S., A.J.S., M.S., R.C.Y., B.L.Y. Other: H.-W.D., B.A.F., C.F. and J.J.M., Allen Reference Atlas generation; J.G.H., data annotation; C.C.O., critical review and manuscript preparation; M.S.B., overall project leadership 2003–2004; A.R.J., overall project leadership 2004–present.

Disclaimer The Nature Publishing Group has a business collaboration with the Allen Institute for the creation and maintenance of the Neuroscience gateway (http://www.brainatlas.org), but has no role in generating or curating the Allen Brain Atlas database content. As always, Nature Editors have been fully independent and solely responsible for the editorial content and peer review of this research article.

Author information

Author notes

  1. Mark S. Boguski
    Present address: Division of Genome and Proteome Sciences, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
  2. Axel Visel
    Present address: Lawrence Berkeley National Laboratory, Genomics Division, MS84-171, 1 Cyclotron Road, Berkeley, California, 94720, USA
  3. Ed S. Lein and Michael J. Hawrylycz: These authors contributed equally to this work.

Authors and Affiliations

  1. Allen Institute for Brain Science, Washington, 98103, Seattle, USA
    Ed S. Lein, Michael J. Hawrylycz, Mikael Ayres, Amy Bensinger, Amy Bernard, Andrew F. Boe, Mark S. Boguski, Kevin S. Brockway, Emi J. Byrnes, Lin Chen, Mei Chi Chin, Jimmy Chong, Brian E. Crook, Chinh N. Dang, Suvro Datta, Nick R. Dee, Aimee L. Desaki, Tsega Desta, Ellen Diep, Tim A. Dolbeare, Matthew J. Donelan, Hong-Wei Dong, Jennifer G. Dougherty, Ben J. Duncan, Amanda J. Ebbert, Lili K. Estin, Casey Faber, Benjamin A. Facer, Shanna R. Fischer, Tim P. Fliss, Cliff Frensley, Sabrina N. Gates, Katie J. Glattfelder, Kevin R. Halverson, Matthew R. Hart, John G. Hohmann, Maureen P. Howell, Darren P. Jeung, Rebecca A. Johnson, Patrick T. Karr, Reena Kawal, Jolene M. Kidney, Rachel H. Knapik, Chihchau L. Kuan, James H. Lake, Annabel R. Laramee, Kirk D. Larsen, Christopher Lau, Tracy A. Lemon, Lon T. Luong, Jesse Michaels, Judith J. Morgan, Rebecca J. Morgan, Marty T. Mortrud, Nerick F. Mosqueda, Lydia L. Ng, Randy Ng, Geralyn J. Orta, Caroline C. Overly, Tu H. Pak, Sheana E. Parry, Sayan D. Pathak, Owen C. Pearson, Ralph B. Puchalski, Zackery L. Riley, Hannah R. Rockett, Stephen A. Rowland, Joshua J. Royall, Nadia R. Sarno, Katherine Schaffnit, Nadiya V. Shapovalova, Taz Sivisay, Clifford R. Slaughterbeck, Simon C. Smith, Kimberly A. Smith, Bryan I. Smith, Andy J. Sodt, Nick N. Stewart, Kenda-Ruth Stumpf, Susan M. Sunkin, Madhavi Sutram, Carey D. Teemer, Carol L. Thompson, Lee R. Varnam, Ray M. Whitlock, Paul E. Wohnoutka, Crissa K. Wolkey, Victoria Y. Wong, Rob C. Young, Brian L. Youngstrom, Xu Feng Yuan, Theresa A. Zwingman & Allan R. Jones
  2. Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Texas, 77030, Houston, USA
    Nancy Ao, Li Chen, Tsuey-Ming Chen, Aneta Czaplinska, Rick Fields, Agnes J. Liang, Ying Liu, Marcos J. Ruiz, Angelene Tam, Christina Thaller, Matthew Wood, Murat B. Yaylaoglu & Bin Zhang
  3. Department of Genes and Behavior, Max Planck Institute of Biophysical Chemistry, 37077, Goettingen, Germany
    Gregor Eichele & Axel Visel

Authors

  1. Ed S. Lein
    You can also search for this author inPubMed Google Scholar
  2. Michael J. Hawrylycz
    You can also search for this author inPubMed Google Scholar
  3. Nancy Ao
    You can also search for this author inPubMed Google Scholar
  4. Mikael Ayres
    You can also search for this author inPubMed Google Scholar
  5. Amy Bensinger
    You can also search for this author inPubMed Google Scholar
  6. Amy Bernard
    You can also search for this author inPubMed Google Scholar
  7. Andrew F. Boe
    You can also search for this author inPubMed Google Scholar
  8. Mark S. Boguski
    You can also search for this author inPubMed Google Scholar
  9. Kevin S. Brockway
    You can also search for this author inPubMed Google Scholar
  10. Emi J. Byrnes
    You can also search for this author inPubMed Google Scholar
  11. Lin Chen
    You can also search for this author inPubMed Google Scholar
  12. Li Chen
    You can also search for this author inPubMed Google Scholar
  13. Tsuey-Ming Chen
    You can also search for this author inPubMed Google Scholar
  14. Mei Chi Chin
    You can also search for this author inPubMed Google Scholar
  15. Jimmy Chong
    You can also search for this author inPubMed Google Scholar
  16. Brian E. Crook
    You can also search for this author inPubMed Google Scholar
  17. Aneta Czaplinska
    You can also search for this author inPubMed Google Scholar
  18. Chinh N. Dang
    You can also search for this author inPubMed Google Scholar
  19. Suvro Datta
    You can also search for this author inPubMed Google Scholar
  20. Nick R. Dee
    You can also search for this author inPubMed Google Scholar
  21. Aimee L. Desaki
    You can also search for this author inPubMed Google Scholar
  22. Tsega Desta
    You can also search for this author inPubMed Google Scholar
  23. Ellen Diep
    You can also search for this author inPubMed Google Scholar
  24. Tim A. Dolbeare
    You can also search for this author inPubMed Google Scholar
  25. Matthew J. Donelan
    You can also search for this author inPubMed Google Scholar
  26. Hong-Wei Dong
    You can also search for this author inPubMed Google Scholar
  27. Jennifer G. Dougherty
    You can also search for this author inPubMed Google Scholar
  28. Ben J. Duncan
    You can also search for this author inPubMed Google Scholar
  29. Amanda J. Ebbert
    You can also search for this author inPubMed Google Scholar
  30. Gregor Eichele
    You can also search for this author inPubMed Google Scholar
  31. Lili K. Estin
    You can also search for this author inPubMed Google Scholar
  32. Casey Faber
    You can also search for this author inPubMed Google Scholar
  33. Benjamin A. Facer
    You can also search for this author inPubMed Google Scholar
  34. Rick Fields
    You can also search for this author inPubMed Google Scholar
  35. Shanna R. Fischer
    You can also search for this author inPubMed Google Scholar
  36. Tim P. Fliss
    You can also search for this author inPubMed Google Scholar
  37. Cliff Frensley
    You can also search for this author inPubMed Google Scholar
  38. Sabrina N. Gates
    You can also search for this author inPubMed Google Scholar
  39. Katie J. Glattfelder
    You can also search for this author inPubMed Google Scholar
  40. Kevin R. Halverson
    You can also search for this author inPubMed Google Scholar
  41. Matthew R. Hart
    You can also search for this author inPubMed Google Scholar
  42. John G. Hohmann
    You can also search for this author inPubMed Google Scholar
  43. Maureen P. Howell
    You can also search for this author inPubMed Google Scholar
  44. Darren P. Jeung
    You can also search for this author inPubMed Google Scholar
  45. Rebecca A. Johnson
    You can also search for this author inPubMed Google Scholar
  46. Patrick T. Karr
    You can also search for this author inPubMed Google Scholar
  47. Reena Kawal
    You can also search for this author inPubMed Google Scholar
  48. Jolene M. Kidney
    You can also search for this author inPubMed Google Scholar
  49. Rachel H. Knapik
    You can also search for this author inPubMed Google Scholar
  50. Chihchau L. Kuan
    You can also search for this author inPubMed Google Scholar
  51. James H. Lake
    You can also search for this author inPubMed Google Scholar
  52. Annabel R. Laramee
    You can also search for this author inPubMed Google Scholar
  53. Kirk D. Larsen
    You can also search for this author inPubMed Google Scholar
  54. Christopher Lau
    You can also search for this author inPubMed Google Scholar
  55. Tracy A. Lemon
    You can also search for this author inPubMed Google Scholar
  56. Agnes J. Liang
    You can also search for this author inPubMed Google Scholar
  57. Ying Liu
    You can also search for this author inPubMed Google Scholar
  58. Lon T. Luong
    You can also search for this author inPubMed Google Scholar
  59. Jesse Michaels
    You can also search for this author inPubMed Google Scholar
  60. Judith J. Morgan
    You can also search for this author inPubMed Google Scholar
  61. Rebecca J. Morgan
    You can also search for this author inPubMed Google Scholar
  62. Marty T. Mortrud
    You can also search for this author inPubMed Google Scholar
  63. Nerick F. Mosqueda
    You can also search for this author inPubMed Google Scholar
  64. Lydia L. Ng
    You can also search for this author inPubMed Google Scholar
  65. Randy Ng
    You can also search for this author inPubMed Google Scholar
  66. Geralyn J. Orta
    You can also search for this author inPubMed Google Scholar
  67. Caroline C. Overly
    You can also search for this author inPubMed Google Scholar
  68. Tu H. Pak
    You can also search for this author inPubMed Google Scholar
  69. Sheana E. Parry
    You can also search for this author inPubMed Google Scholar
  70. Sayan D. Pathak
    You can also search for this author inPubMed Google Scholar
  71. Owen C. Pearson
    You can also search for this author inPubMed Google Scholar
  72. Ralph B. Puchalski
    You can also search for this author inPubMed Google Scholar
  73. Zackery L. Riley
    You can also search for this author inPubMed Google Scholar
  74. Hannah R. Rockett
    You can also search for this author inPubMed Google Scholar
  75. Stephen A. Rowland
    You can also search for this author inPubMed Google Scholar
  76. Joshua J. Royall
    You can also search for this author inPubMed Google Scholar
  77. Marcos J. Ruiz
    You can also search for this author inPubMed Google Scholar
  78. Nadia R. Sarno
    You can also search for this author inPubMed Google Scholar
  79. Katherine Schaffnit
    You can also search for this author inPubMed Google Scholar
  80. Nadiya V. Shapovalova
    You can also search for this author inPubMed Google Scholar
  81. Taz Sivisay
    You can also search for this author inPubMed Google Scholar
  82. Clifford R. Slaughterbeck
    You can also search for this author inPubMed Google Scholar
  83. Simon C. Smith
    You can also search for this author inPubMed Google Scholar
  84. Kimberly A. Smith
    You can also search for this author inPubMed Google Scholar
  85. Bryan I. Smith
    You can also search for this author inPubMed Google Scholar
  86. Andy J. Sodt
    You can also search for this author inPubMed Google Scholar
  87. Nick N. Stewart
    You can also search for this author inPubMed Google Scholar
  88. Kenda-Ruth Stumpf
    You can also search for this author inPubMed Google Scholar
  89. Susan M. Sunkin
    You can also search for this author inPubMed Google Scholar
  90. Madhavi Sutram
    You can also search for this author inPubMed Google Scholar
  91. Angelene Tam
    You can also search for this author inPubMed Google Scholar
  92. Carey D. Teemer
    You can also search for this author inPubMed Google Scholar
  93. Christina Thaller
    You can also search for this author inPubMed Google Scholar
  94. Carol L. Thompson
    You can also search for this author inPubMed Google Scholar
  95. Lee R. Varnam
    You can also search for this author inPubMed Google Scholar
  96. Axel Visel
    You can also search for this author inPubMed Google Scholar
  97. Ray M. Whitlock
    You can also search for this author inPubMed Google Scholar
  98. Paul E. Wohnoutka
    You can also search for this author inPubMed Google Scholar
  99. Crissa K. Wolkey
    You can also search for this author inPubMed Google Scholar
  100. Victoria Y. Wong
    You can also search for this author inPubMed Google Scholar
  101. Matthew Wood
    You can also search for this author inPubMed Google Scholar
  102. Murat B. Yaylaoglu
    You can also search for this author inPubMed Google Scholar
  103. Rob C. Young
    You can also search for this author inPubMed Google Scholar
  104. Brian L. Youngstrom
    You can also search for this author inPubMed Google Scholar
  105. Xu Feng Yuan
    You can also search for this author inPubMed Google Scholar
  106. Bin Zhang
    You can also search for this author inPubMed Google Scholar
  107. Theresa A. Zwingman
    You can also search for this author inPubMed Google Scholar
  108. Allan R. Jones
    You can also search for this author inPubMed Google Scholar

Corresponding authors

Correspondence toEd S. Lein or Allan R. Jones.

Ethics declarations

Competing interests

Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplemental Methods 1

Detailed methodologies for tissue processing, probe design and generation, data generation, and image acquisition used for the Allen Brain Atlas project (PDF 1587 kb)

Supplemental Methods 2

Detailed methodologies for informatics-based image quantification and mapping of ISH data to a common 3D coordinate system for genome-wide analysis (DOC 25603 kb)

Supplemental Methods 3

Detailed methodologies used to generate the Allen Reference Atlas (PDF 559 kb)

Supplemental Methods 4

Description of methods used for voxel-based correlation analysis (DOC 41 kb)

Supplemental Data 1

Comparison of non-isotopic in situ hybridization (ISH) data generated for the Allen Brain Atlas project to comparable radioactive ISH data from other sources (DOC 2418 kb)

Supplemental Data 2

Side-by-side image comparison of non-isotopic in situ hybridization (ISH) data generated for the Allen Brain Atlas project to comparable radioactive ISH data. Accompanies Supplemental Data 1 (PDF 19230 kb)

Supplemental Data 3

Control data demonstrating the reproducibility of the ABA ISH platform across conditions and across the duration of the ABA project (PDF 4775 kb)

Supplemental Data 4

Comparison of expression patterns of the ligand-gated ion channel family to available literature and other data sources, as well as methodology for fine-detailed expert annotation of the ligand-gated ion channel family in the neocortex (DOC 412 kb)

Supplemental Data 5

Detailed expert annotation of the complete ligand-gated ion channel family in layers of the neocortex. Accompanies Supplemental Data 4 (XLS 44 kb)

Supplemental Figure 1

Genome-wide analysis of expression level vs. percentage of expressing cells in 12 major brain regions (JPG 840 kb)

Supplementary Table 1

Genes enriched in major cell populations in the brain (neurons, oligodendrocytes, astrocytes, and choroid plexus cells) identified through correlation-based searches seeded with cell-type specific gene expression patterns. Also included are genes with apparent ubiquity as well as genes that do not have detectable expression in the brain (XLS 184 kb)

Supplemental Table 2

Gene Ontology (GO) categories over-represented in genes enriched in major neural cell types and in genes that are either apparently ubiquitous or not expressed. Accompanies Supplemental Table 1 (XLS 612 kb)

Supplemental Table 3

Genes identified as the most specific for each of 12 different major brain regions (XLS 198 kb)

Supplemental Table 4

Genes displaying mRNA targeting to dendrites (neurons) or processes (non-neuronal cells) (XLS 37 kb)

Rights and permissions

About this article

Cite this article

Lein, E., Hawrylycz, M., Ao, N. et al. Genome-wide atlas of gene expression in the adult mouse brain.Nature 445, 168–176 (2007). https://doi.org/10.1038/nature05453

Download citation