Cell type-specific transcriptomics in the brain

Journal of Neuroscience

Volumn 31, Issue 19, 2011, Pages 6939-6943

  Okaty, Benjamin W ^a   Sugino, Ken ^a   Nelson, Sacha B ^a  

^a BRANDEIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME;

ARTICLE; BRAIN FUNCTION; CELL TYPE; DNA MICROARRAY; FLUORESCENCE ACTIVATED CELL SORTING; GENE AMPLIFICATION; GENE CONTROL; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RNA SEQUENCE; SERIAL ANALYSIS OF GENE EXPRESSION; TRANSCRIPTOMICS;

ANIMALS; BRAIN; GENE EXPRESSION PROFILING; NEUROGLIA; NEURONS;

EID: 79956315360     PISSN: 02706474     EISSN: 15292401     Source Type: Journal    
DOI: 10.1523/JNEUROSCI.0626-11.2011     Document Type: Article

References (35)

1. Arlotta P, Molyneaux BJ, Chen J, Inoue J, Kominami R, Macklis JD (2005) Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron 45:207-221.
2. Barres BA, Silverstein BE, Corey DP, Chun LL (1988) Immunological, morphological, and electrophysiological variation among retinal ganglion cells purified by panning. Neuron 1:791-803.
3. Barres BA, Hart IK, Coles HS, Burne JF, Voyvodic JT, Richardson WD, Raff MC (1992) Cell death and control of cell survival in the oligodendrocyte lineage. Cell 70:31-46.
4. Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, Christopherson KS, Xing Y, Lubischer JL, Krieg PA, Krupenko SA, Thompson WJ, Barres BA (2008) A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci 28:264-278.
5. Chattopadhyaya B, Di Cristo G, Higashiyama H, Knott GW, Kuhlman SJ, Welker E, Huang ZJ (2004) Experience and activity-dependent maturation of perisomatic GABAergic innervation in primary visual cortex during a postnatal critical period. J Neurosci 24:9598-9611.
6. Darnell JC, Fraser CE, Mostovetsky O, Darnell RB (2009) Discrimination of common and unique RNA-binding activities among Fragile X mental retardation protein paralogs. Human Molecular Genetics 18:3164-3177.
7. Dougherty JD, Schmidt EF, Nakajima M, Heintz N (2010) Analytical approaches to RNA profiling data for the identification of genes enriched in specific cells. Nucleic Acids Res 38:4218-4230.
8. Doyle JP, Dougherty JD, Heiman M, Schmidt EF, Stevens TR, Ma G, Bupp S, Shrestha P, Shah RD, Doughty ML, Gong S, Greengard P, Heintz N (2008) Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135:749-762.
9. Dugas JC, Mandemakers W, Rogers M, Ibrahim A, Daneman R, Barres BA (2008) A novel purification method for CNS projection neurons leads to the identification of brain vascular cells as a source of trophic support for corticospinal motor neurons. J Neurosci 28:8294-8305.
10. Feng G, Mellor RH, Bernstein M, Keller-Peck C, Nguyen QT, Wallace M, Nerbonne JM, Lichtman JW, Sanes JR (2000) Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP. Neuron 28:41-51.
11. Gong S, Zheng C, Doughty ML, Losos K, Didkovsky N, Schambra UB, Nowak NJ, Joyner A, Leblanc G, Hatten ME, Heintz N (2003) A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature 425:917-925.
12. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of linc RNAs. Nat Biotechnol 28:503-510.
13. Heiman M, Schaefer A, Gong S, Peterson JD, Day M, Ramsey KE, Suárez-Fariñas M, Schwarz C, Stephan DA, Surmeier DJ, Greengard P, Heintz N (2008) A translational profiling approach for the molecular characterization of CNS cell types. Cell 135:738-748.
14. Hempel CM, Sugino K, Nelson SB (2007) A manual method for the purification of fluorescently labeled neurons from the mammalian brain. Nat Protoc 2:2924-2929.
15. Janes KA, Wang CC, Holmberg KJ, Cabral K, Brugge JS (2010) Identifying single-cell molecular programs by stochastic profiling. Nat Methods 7:311-317.
16. Kuhlman SJ, Huang ZJ (2008) High-resolution labeling and functional manipulation of specific neuron types in mouse brain by Creactivated viral gene expression. PLoS One 3:e2005.
17. Kurimoto K, Saitou M (2010) Single-cell cDNA microarray profiling of complex biological processes of differentiation. Curr Opin Genet Dev 20:470-477.
18. Lobo MK, Karsten SL, Gray M, Geschwind DH, Yang XW (2006) FACS-array profiling of striatal projection neuron subtypes in juvenile and adult mouse brains. Nat Neurosci 9:443-452.
19. Madisen L, Zwingman TA, Sunkin SM, Oh SW, Zariwala HA, Gu H, Ng LL, Palmiter RD, Hawrylycz MJ, Jones AR, Lein ES, Zeng H (2010) A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat Neurosci 13:133-140.
20. Marsh ED, Minarcik J, Campbell K, Brooks-Kayal AR, Golden JA (2008) FACS-array gene expression analysis during early development of mouse telencephalic interneurons. Dev Neurobiol 68:434-445.
21. Martina M, Schultz JH, Ehmke H, Monyer H, Jonas P (1998) Functional and molecular differences between voltage-gated K+ channels of fast-spiking interneurons and pyramidal neurons of rat hippocampus. J Neurosci 18:8111-8125.
22. Miyoshi G, Fishell G (2006) Directing neuronspecific transgene expression in the mouse CNS. Curr Opin Neurobiol 16:577-584.
23. Okaty BW, Miller MN, Sugino K, Hempel CM, Nelson SB (2009) Transcriptional and electrophysiological maturation of neocortical fast-spiking GABAergic interneurons. J Neurosci 29:7040-7052.
24. Okaty BW, Sugino K, Nelson SB (2011) A quantitative comparison of cell-type-specific microarray gene expression profiling methods in the mouse brain. PLoS One 6:e16493.
25. Oliva AA Jr, Jiang M, Lam T, Smith KL, Swann JW (2000) Novel hippocampal interneuronal subtypes identified using transgenic mice that express green fluorescent protein in GABAergic interneurons. J Neurosci 20:3354-3368.
26. Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM (2010a) Digital transcriptome profiling from attomole-level RNA samples. Genome Res 20:519-525.
27. Ozsolak F, Ting DT, Wittner BS, Brannigan BW, Paul S, Bardeesy N, Ramaswamy S, Milos PM, Haber DA (2010b) Amplification-free digital gene expression profiling from minute cell quantities. Nat Methods 7:619-621.
28. Raj A, van Oudenaarden A (2009) Single-molecule approaches to stochastic gene expression. Annu Rev Biophys 38:255-270.
29. Rossner MJ, Hirrlinger J, Wichert SP, Boehm C, Newrzella D, Hiemisch H, Eisenhardt G, Stuenkel C, von Ahsen O, Nave KA (2006) Global transcriptome analysis of genetically identified neurons in the adult cortex. J Neurosci 26:9956-9966.
30. Sanz E, Yang L, Su T, Morris DR, McKnight GS, Amieux PS (2009) Cell-type-specific isolation of ribosome-associated mRNA from complex tissues. Proc Natl Acad Sci U S A 106:13939-13944.
31. Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci U S A 89:8794-8797.
32. Subkhankulova T, Yano K, Robinson HP, Livesey FJ (2010) Grouping and classifying electrophysiologically-defined classes of neocortical neurons by single cell, whole-genome expression profiling. Front Mol Neurosci 3:10.
33. Sugino K, Hempel CM, Miller MN, Hattox AM, Shapiro P, Wu C, Huang ZJ, Nelson SB (2006) Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nat Neurosci 9:99-107.
34. Surmeier DJ, Song WJ, Yan Z (1996) Coordinated expression of dopamine receptors in neostriatal medium spiny neurons. J Neurosci 16:6579-6591.
35. Toledo-Rodriguez M, Blumenfeld B, Wu C, Luo J, Attali B, Goodman P, Markram H (2004) Correlation maps allow neuronal electrical properties to be predicted from single-cell gene expression profiles in rat neocortex. Cereb Cortex 14:1310-1327.