Genome-wide gene expression profiling of nucleus accumbens neurons projecting to ventral pallidum using both microarray and transcriptome sequencing

Frontiers in Neuroscience

Volumn , Issue AUG, 2011, Pages

  Chen, Hao ^a   Liu, Zhimin ^a   Gong, Suzhen ^a   Wu, Xingjun ^a   Taylor, William L ^a   Williams, Robert W ^a   Matta, Shannon G ^a   Sharp, Burt M ^a  

^a UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

Author keywords

GABA; GABAergic; Laser capture microdissection; Microarray; Nucleus accumbens; RNA sequencing; Transcriptome sequencing

Indexed keywords

EID: 84855826245     PISSN: 16624548     EISSN: 1662453X     Source Type: Journal    
DOI: 10.3389/fnins.2011.00098     Document Type: Article

References (20)

1. Bradford, J. R., Hey, Y., Yates, T., Li, Y., Pepper, S. D., and Miller, C. J. (2010). A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics 11, 282. doi: 10.1186/1471-2164-11-282
2. Costa, V., Angelini, C., De Feis, I., and Ciccodicola, A. (2010). Uncovering the complexity of transcriptomes with RNA-Seq. J. Biomed. Biotechnol. 2010, 853916.
3. David, M., Dzamba, M., Lister, D., Ilie, L., and Brudno, M. (2011). SHRiMP2: sensitive yet practical SHort Read Mapping. Bioinformatics 27, 1011-1012.
4. El Mestikawy, S., Wallen-Mackenzie, A., Fortin, G. M., Descarries, L., and Trudeau, L. E. (2011). From glutamate co-release to vesicular synergy: vesicular glutamate transporters. Nat. Rev. Neurosci. 12, 204-216.
5. Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini, A. J., Sawitzki, G., Smith, C., Smyth, G., Tierney, L., Yang, J. Y., and Zhang, J. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80.
6. Johannes, F., Wardenaar, R., Colome-Tatche, M., Mousson, F., De Graaf, P., Mokry, M., Guryev, V., Timmers, H. T., Cuppen, E., and Jansen, R. C. (2010). Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. Bioinformatics 26, 1000-1006.
7. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079.
8. Lupski, J. R., Reid, J. G., Gonzaga-Jauregui, C., Rio Deiros, D., Chen, D. C., Nazareth, L., Bainbridge, M., Dinh, H., Jing, C., Wheeler, D. A., Mcguire, A. L., Zhang, F., Stankiewicz, P., Halperin, J. J., Yang, C., Gehman, C., Guo, D., Irikat, R. K., Tom, W., Fantin, N. J., Muzny, D. M., and Gibbs, R. A. (2010). Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N. Engl. J. Med. 362, 1181-1191.
9. Mane, S. P., Evans, C., Cooper, K. L., Crasta, O. R., Folkerts, O., Hutchison, S. K., Harkins, T. T., Thierry-Mieg, D., Thierry-Mieg, J., and Jensen, R. V. (2009). Transcriptome sequencing of the microarray quality control (MAQC) RNA reference samples using next generation sequencing. BMC Genomics 10, 264. doi: 10.1186/1471-2164-10-264
10. Mortazavi, A., Williams, B. A., Mccue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628.
11. Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., and Snyder, M. (2008). The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344-1349.
12. Okaty, B. W., Sugino, K., and Nelson, S. B. (2011). A quantitative comparison of cell-type-specific microarray gene expression profiling methods in the mouse brain. PLoS ONE 6, e16493. doi: 10.1371/journal.pone.0016493
13. Okoniewski, M. J., and Miller, C. J. (2006). Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinformatics 7, 276. doi: 10.1186/1471-2105-7-276
14. Ozsolak, F., and Milos, P. M. (2011). RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet. 12, 87-98.
15. Quinlan, A. R., and Hall, I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842.
16. Roberts, A., Trapnell, C., Donaghey, J., Rinn, J. L., and Pachter, L. (2011). Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol. 12, R22.
17. Rumble, S. M., Lacroute, P., Dalca, A. V., Fiume, M., Sidow, A., and Brudno, M. (2009). SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol. 5, e1000386. doi: 10.1371/journal. pcbi.1000386
18. Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., Van Baren, M. J., Salzberg, S. L., Wold, B. J., and Pachter, L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515.
19. Wang, Z., Gerstein, M., and Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63.
20. Wilhelm, B. T., and Landry, J. R. (2009). RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods 48, 249-257.