A high-throughput method for Illumina RNA-Seq library preparation

Frontiers in Plant Science

Volumn 3, Issue AUG, 2012, Pages

  Kumar, Ravi ^a   Ichihashi, Yasunori ^a   Kimura, Seisuke ^a,b   Chitwood, Daniel H ^a   Headland, Lauren R ^a   Peng, Jie ^a   Maloof, Julin N ^a   Sinha, Neelima R ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b KYOTO SANGYO UNIVERSITY   (Japan)

Author keywords

cDNA fragmentation; High throughput; Illumina; mRNA isolation; Multiplexing; RNA Seq; Sequencing

Indexed keywords

EID: 84870935147     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2012.00202     Document Type: Article

References (28)

1. Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate-a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57, 289-300.
2. Chen, H., and Boutros, P. C. (2011). VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics 12, 35.
3. The Tomato Genome Consortium. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635-641.
4. Craig, D. W., Pearson, J. V., Szelinger, S., Sekar, A., Redman, M., Corneveaux, J. J., Pawlowski, T. L., Laub, T., Nunn, G., Stephan, D. A., Homer, N., and Huentelman, M. J. (2008). Identification of genetic variants using bar-coded multiplexed sequencing. Nat. Methods 5, 887-893.
5. Fisher, S., Barry, A., Abreu, J., Minie, B., Nolan, J., Delorey, T. M., Young, G., Fennell, T. J., Allen, A., Ambrogio, L., Berlin, A. M., Blumenstiel, B., Cibulskis, K., Friedrich, D., Johnson, R., Juhn, F., Reilly, B., Shammas, R., Stalker, J., Sykes, S. M., Thompson, J., Walsh, J., Zimmer, A., Zwirko, Z., Gabriel, S., Nicol, R., and Nusbaum, C. (2011). A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol. 12, R1.
6. Fox-Walsh, K., Davis-Turak, J., Zhou, Y., Li, H., and Fu, X.-D. (2011). A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3′ end formation. Genomics 98, 266-271.
7. Goff, S. A., Vaughn, M., Mckay, S., Lyons, E., Stapleton, A. E., Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M., Jordan, C., Skidmore, E., Dooley, R., Cazes, J., Mclay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W. H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S.-J., Kvilekval, K., Manjunath, B. S., Tannen, V., Stamatakis, A., Sanderson, M., Welch, S. M., Cranston, K., Soltis, P., Soltis, D., O'meara, B., Ane, C., Brutnell, T., Kleibenstein, D. J., White, J. W., Leebens-Mack, J., Donoghue, M. J., Spalding, E. P., Vision, T. J., Myers, C. R., Lowenthal, D., Enquist, B. J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., and Stanzione, D. (2011). The iPlant Collaborative: cyberinfrastructure for plant biology. Front. Plant Sci. 2:34. doi:10.3389/fpls.2011.00034
8. Hansen, K. D., Brenner, S. E., and Dudoit, S. (2010). Biases in illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res. 38, e131.
9. Hawkins, T. L., O'Connor-Morin, T., Roy, A., and Santillan, C. (1994). DNA purification and isolation using a solid-phase. Nucleic Acids Res. 22, 4543-4544.
10. Langmead, B., Trapnell, C., Pop, M., and Salzberg, S. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25.
11. Lennon, N. J., Lintner, R. E., Anderson, S., Alvarez, P., Barry, A., Brockman, W., Daza, R., Erlich, R. L., Giannoukos, G., and Green, L. (2010). A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454. Genome Biol. 11, R15.
12. Levin, J. Z., Yassour, M., Adiconis, X., Nusbaum, C., Thompson, D. A., Friedman, N., Gnirke, A., and Regev, A. (2010). Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709-715.
13. Mader, U., Nicolas, P., Richard, H., Bessieres, P., and Aymerich, S. (2011). Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods. Curr. Opin. Biotechnol. 22, 32-41.
14. Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., and Gilad, Y. (2008). RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509-1517.
15. Meyer, M., and Kircher, M. (2010). Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. pdb prot5448.
16. Nagalakshmi, U., Waern, K., and Snyder, M. (2010). RNA-Seq: a method for comprehensive transcriptome analysis. Curr. Protoc. Mol. Biol. Chapter 4, Unit 4.11.1-13.
17. Ozsolak, F., and Milos, P. M. (2011). RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet. 12, 87-98.
18. Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H., and Soldatov, A. (2009). Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 37, e123.
19. Quail, M. A., Kozarewa, I., Smith, F., Scally, A., Stephens, P. J., Durbin, R., Swerdlow, H., and Turner, D. J. (2008). A large genome center's improvements to the illumina sequencing system. Nat. Methods 5, 1005-1010.
20. R Development Core Team. (2011). R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing.
21. Robinson, M. D., and Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25.
22. Wang, L., Feng, Z., Wang, X., and Zhang, X. (2009). DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26, 136-138.
23. Wang, L., Si, Y., Dedow, L. K., Shao, Y., Liu, P., and Brutnell, T. P. (2011a). A low-cost library construction protocol and data analysis pipeline for illumina-based strand-specific multiplex RNA-seq. PLoS ONE 6, e26426. doi:10.1371/journal.pone.0026426
24. Wang, Y., Ghaffari, N., Johnson, C., Braga-Neto, U., Wang, H., Chen, R., and Zhou, H. (2011b). Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. BMC Bioinformatics 12, S5.
25. Weigel, D., and Mott, R. (2009). The 1001 genomes project for Arabidopsis thaliana. Genome Biol. 10, 107.
26. Wickham, H. (2009). ggplot2: Elegant Graphics for Data Analysis. New York: Springer.
27. Wilhelm, B. T., Marguerat, S., Goodhead, I., and Bahler, J. (2010). Defining transcribed regions using RNA-seq. Nat. Protoc. 5, 255-266.
28. Zhong, S., Joung, J. G., Zheng, Y., Chen, Y. R., Liu, B., Shao, Y., Xiang, J. Z., Fei, Z., and Giovannoni, J. J. (2011). High-throughput illumina strand-specific RNA sequencing library preparation. Cold Spring Harb. Protoc. 2011, 940-949.