A quantitative comparison of cell-type-specific microarray gene expression profiling methods in the mouse brain

PLoS ONE

Volumn 6, Issue 1, 2011, Pages

  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;

ANIMAL TISSUE; ARTICLE; BRAIN TISSUE; CELL TYPE; CONTAMINATION; CONTROLLED STUDY; DNA MICROARRAY; FLUORESCENCE ACTIVATED CELL SORTING; GENE EXPRESSION PROFILING; IMMEDIATE EARLY GENE; IMMUNOPANNING; LASER CAPTURE MICRODISSECTION; MOUSE; NONHUMAN; PURIFICATION; QUANTITATIVE ANALYSIS; TRANSLATING RIBOSOME AFFINITY PURIFICATION; ANIMAL; BRAIN; COMPARATIVE STUDY; CYTOLOGY; GENETIC TRANSCRIPTION; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MICROARRAY ANALYSIS; NERVE CELL; PROTEIN SYNTHESIS; REPRODUCIBILITY; STANDARD; TISSUE DISTRIBUTION;

ANIMALS; BRAIN; GENE EXPRESSION PROFILING; MICE; MICROARRAY ANALYSIS; NEURONS; PROTEIN BIOSYNTHESIS; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; TISSUE DISTRIBUTION; TRANSCRIPTION, GENETIC;

EID: 79551520605     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016493     Document Type: Article

References (31)

1. Chung CY, Seo H, Sonntag KC, Brooks A, Lin L, et al. (2005) Cell type-specific gene expression of midbrain dopaminergic neurons reveals molecules involved in their vulnerability and protection. Hum Mol Genet 14: 1709-1725.
2. Rossner MJ, Hirrlinger J, Wichert SP, Boehm C, Newrzella D, et al. (2006) Global transcriptome analysis of genetically identified neurons in the adult cortex. J Neurosci 26: 9956-9966.
3. Doyle JP, Dougherty JD, Heiman M, Schmidt EF, Stevens TR, et al. (2008) Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135: 749-762.
4. Heiman M, Schaefer A, Gong S, Peterson JD, Day M, et al. (2008) A translational profiling approach for the molecular characterization of CNS cell types. Cell 135: 738-748.
5. Arlotta P, Molyneaux BJ, Chen J, Inoue J, Kominami R, et al. (2005) Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron 45: 207-221.
6. Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, et al. (2008) A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci 28: 264-278.
7. 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.
8. Sugino K, Hempel CM, Miller MN, Hattox AM, Shapiro P, et al. (2006) Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nat Neurosci 9: 99-107.
9. Tullai JW, Schaffer ME, Mullenbrock S, Sholder G, Kasif S, et al. (2007) Immediate-early and delayed primary response genes are distinct in function and genomic architecture. J Biol Chem 282: 23981-23995.
10. Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S (2006) Stochastic mRNA synthesis in mammalian cells. Plos Biology 4: 1707-1719.
11. Raj A, van Oudenaarden A (2009) Single-Molecule Approaches to Stochastic Gene Expression. Annual Review of Biophysics 38: 255-270.
12. Sanchez A, Kondev J (2008) Transcriptional control of noise in gene expression. Proceedings of the National Academy of Sciences of the United States of America 105: 5081-5086.
13. Stahlberg A, Bengtsson M (2010) Single-cell gene expression profiling using reverse transcription quantitative real-time PCR. Methods 50: 282-288.
14. Chattopadhyaya B, Di Cristo G, Higashiyama H, Knott GW, Kuhlman SJ, et al. (2004) Experience and activity-dependent maturation of perisomatic GABAergic innervation in primary visual cortex during a postnatal critical period. J Neurosci 24: 9598-9611.
15. Rong Y, Wang T, Morgan JI (2004) Identification of candidate Purkinje cellspecific markers by gene expression profiling in wild-type and pcd(3J) mice. Brain Res Mol Brain Res 132: 128-145.
16. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, et al. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100: 3889-3894.
17. Beyer A, Hollunder J, Nasheuer HP, Wilhelm T (2004) Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics 3: 1083-1092.
18. Brockmann R, Beyer A, Heinisch JJ, Wilhelm T (2007) Posttranscriptional expression regulation: what determines translation rates? PLoS Comput Biol 3: e57.
19. Andreassi C, Riccio A (2009) To localize or not to localize: mRNA fate is in 39UTR ends. Trends Cell Biol 19: 465-474.
20. Pesole G, Mignone F, Gissi C, Grillo G, Licciulli F, et al. (2001) Structural and functional features of eukaryotic mRNA untranslated regions. Gene 276: 73-81.
21. Johnson WE, Li C, Rabinovic A (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8: 118-127.
22. Martin KC, Ephrussi A (2009) mRNA localization: gene expression in the spatial dimension. Cell 136: 719-730.
23. Sossin WS, DesGroseillers L (2006) Intracellular trafficking of RNA in neurons. Traffic 7: 1581-1589.
24. Arava Y, Boas FE, Brown PO, Herschlag D (2005) Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res 33: 2421-2432.
25. Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, et al. (2009) Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol 7: e1000238.
26. Winden KD, Oldham MC, Mirnics K, Ebert PJ, Swan CH, et al. (2009) The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol 5: 291.
27. Geschwind DH, Konopka G (2009) Neuroscience in the era of functional genomics and systems biology. Nature 461: 908-915.
28. 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.
29. Bahn S, Augood SJ, Ryan M, Standaert DG, Starkey M, et al. (2001) Gene expression profiling in the post-mortem human brain-no cause for dismay. J Chem Neuroanat 22: 79-94.
30. Bernard R, Kerman IA, Meng F, Evans SJ, Amrein I, et al. (2009) Gene expression profiling of neurochemically defined regions of the human brain by in situ hybridization-guided laser capture microdissection. J Neurosci Methods 178: 46-54.
31. Ordway GA, Szebeni A, Duffourc MM, Dessus-Babus S, Szebeni K (2009) Gene expression analyses of neurons, astrocytes, and oligodendrocytes isolated by laser capture microdissection from human brain: detrimental effects of laboratory humidity. J Neurosci Res 87: 2430-2438.