About Neuroseq

NeuroSeq (2012-2016) was an interdisciplinary effort to characterize the transcriptional state of defined neural cell types in fly and mouse using next-generation sequencing and new approaches for purifying individual cell types. NeuroSeq-mouse (presented here) used manual sorting of fluorescently labeled neurons (ref 1) representing >175 different cell types to prepare libraries for Illumina sequencing. Most cell types were isolated from mouse strains produced as part of the GENSAT (ref 2) and Brandeis Enhancer Trap (ref 3) projects. NeuroSeq also contributed to transcriptional analyses of cell types in the hippocampus (ref 4,5) and hypothalamus (ref 6,7). Some of this data is aggregated here together with previously published tissue-specific RNA-seq data (ref 8-11). A paper describing the NeuroSeq resource and resulting analyses is in preparation.


  1. C.M. Hempel, K. Sugino, S.B. Nelson.
    A manual method for the purification of fluorescently labeled neurons from the mammalian brain.
    Nat Protoc 2, 2924–2929 (2007). doi: 10.1038/nprot.2007.416
  2. Gong S, Zheng C, Doughty ML, Losos K, Didkovsky N, Schambra UB, Nowak NJ, Joyner A, Leblanc G, Hatten ME, Heintz N.
    A gene expression atlas of the central nervous system based on bacterial artificial chromosomes.
    Nature 425:917-25 (2003). doi: 10.1038/nature02033
  3. Shima Y, Sugino K, Hempel CM, Shima M, Taneja P, Bullis JB, Mehta S, Lois C, Nelson SB.
    A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types.
    eLife 5. pii: e13503 (2016) doi: 10.7554/eLife.13503
  4. Cembrowski MS, Wang L, Sugino K, Shields BC, Spruston N.
    Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.
    eLife 5 pii: e14997 (2016). doi: 10.7554/eLife.14997
  5. Cembrowski MS, Bachman JL, Wang L, Sugino K, Shields BC, Spruston N.
    Spatial Gene-Expression Gradients Underlie Prominent Heterogeneity of CA1 Pyramidal Neurons.
    Neuron. 2016 Jan 20;89(2):351-68. doi: 10.1016/j.neuron.2015.12.013
  6. Branco T, Tozer A, Magnus CJ, Sugino K, Tanaka S, Lee AK, Wood JN, Sternson SM
    Near-perfect synaptic integration by Nav1.7 in hypothalamic neurons regulates body weight.
    Cell 165:1749-61 (2016) doi: 10.1016/j.cell.2016.05.019
  7. Henry FE, Sugino K, Tozer A, Branco T, Sternson SM
    Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss.
    eLife. 4.(2015) doi: 10.7554/eLife.09800
  8. Zhang Y, Chen K, Sloan SA, Bennett ML, Scholze AR, O'Keeffe S, Phatnani HP, Guarnieri P, Caneda C, Ruderisch N, Deng S, Liddelow SA, Zhang C, Daneman R, Maniatis T, Barres BA, Wu JQ.
    An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex.
    J Neurosci. 2014 Sep 3;34(36):11929-47. doi: 10.1523/JNEUROSCI.1860-14.2014
  9. He X, Zhang L, Chen Y, Remke M, Shih D, Lu F, Wang H, Deng Y, Yu Y, Xia Y, Wu X, Ramaswamy V, Hu T, Wang F, Zhou W, Burns DK, Kim SH, Kool M, Pfister SM, Weinstein LS, Pomeroy SL, Gilbertson RJ, Rubin JB, Hou Y, Wechsler-Reya R, Taylor MD, Lu QR.
    The G protein α subunit Gαs is a tumor suppressor in Sonic hedgehog-driven medulloblastoma.
    Nat Med. 2014 Sep;20(9):1035-42. doi: 10.1038/nm.3666.
  10. Warren BL, Vialou VF, Iñiguez SD, Alcantara LF, Wright KN, Feng J, Kennedy PJ, Laplant Q, Shen L, Nestler EJ, Bolaños-Guzmán CA.
    Neurobiological sequelae of witnessing stressful events in adult mice.
    Biol Psychiatry. 2013 Jan 1;73(1):7-14. doi: 10.1016/j.biopsych.2012.06.006.
  11. Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, Durbin R, Jackson IJ, Czechanski A, Guerra-Assunção JA, Donahue LR, Reinholdt LG, Payseur BA, Ponting CP, Birney E, Flint J, Adams DJ.
    Mouse genomic variation and its effect on phenotypes and gene regulation.
    Nature. 2011 Sep 14;477(7364):289-94. doi: 10.1038/nature10413.

© 2016 Janelia Research Campus | 19700 Helix Drive, Ashburn, VA 20147 | (571) 209-4000