Sequencing and Characterization of Divergent Marbling Levels in the Beef Cattle (Longissimus dorsi Muscle) Transcriptome |
Chen, Dong
(College of Animal Science and Technology, China Agricultural University)
Li, Wufeng (College of Life Science, Shanxi Agriculture University) Du, Min (Department of Animal Sciences, Washington State University) Wu, Meng (Snowdragon Beef Co., Ltd.) Cao, Binghai (College of Animal Science and Technology, China Agricultural University) |
1 | Kim, D., G. Pertea, C. Trapnell, H. Pimentel, R. Kelley, and S. L. Salzberg. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14:R36. DOI ScienceOn |
2 | Langmead, B. and S. L. Salzberg. 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9:357-359. DOI ScienceOn |
3 | Marioni, J. C., C. E. Mason, S. M. Mane, M. Stephens, and Y. Gilad. 2008. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18:1509-1517. DOI ScienceOn |
4 | Nagalakshmi, U., Z. Wang, K. Waern, C. Shou, D. Raha, M. Gerstein, and M. Snyder. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349. DOI ScienceOn |
5 | Reecy, J., D. M. Spurlock, and C. H. Stahl. 2006. Gene expression profiling: insights into skeletal muscle growth and development. J. Anim. Sci. 84:E150-E154. DOI |
6 | 't Hoen, P. A. C., Y. Ariyurek, H. H. Thygesen, E. Vreugdenhil, R. H. A. M. Vossen, R. X. de Menezes, J. M. Boer, G-J. B. van Ommen, and J. T. den Dunnen. 2008. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucl. Acids Res. 36:e141. DOI ScienceOn |
7 | Trapnell, C., A. Roberts, L. Goff, G. Pertea, D. Kim, D. R. Kelley, H. Pimentel, S. L. Salzberg, J. L. Rinn, and L. Pachter. 2012. Differential gene and transcript expression analysis of RNAseq experiments with TopHat and Cufflinks. Nat. Protoc. 7:562-578. DOI ScienceOn |
8 | Wang, Z., M. Gerstein, and M. Snyder. 2009. RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 10:57-63. DOI ScienceOn |
9 | Wang, Y. H., N. I. Bower, A. Reverter, S. H. Tan, N. De Jager, R. Wang, S. M. McWilliam, L. M. Cafe, P. L. Greenwood, and S. A. Lehnert. 2009. Gene expression patterns during intramuscular fat development in cattle. J. Anim. Sci. 87:119-130. DOI |
10 | Wang, Y. H., K. A. Byrne, A. Reverter, G. S. Harper, M. Taniguchi, S. M. McWilliam, H. Mannen, K. Oyama, and S. A. Lehnert. 2005. Transcriptional profiling of skeletal muscle tissue from two breeds of cattle. Mamm. Genome 16:201-210. DOI |
11 | Werner, T. 2010. Next generation sequencing in functional genomics. Brief. Bioinform. 11:499-511. DOI ScienceOn |
12 | Grobet, L., L. J. R. Martin, D. Poncelet, D. Pirottin, B. Brouwers, J. Riquet, A. Schoeberlein, S. Dunner, F. Menissier, J. Massabanda, R. Fries, R. Hanset, and M. Georges. 1997. A deletion in the bovine myostatin gene causes the doublemuscled phenotype in cattle. Nat. Genet. 17:71-74. DOI ScienceOn |
13 | Cox, M. P., D. A. Peterson, and P. J. Biggs. 2010. SolexaQA: At-aglance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11:485. DOI ScienceOn |
14 | Baldwin, R. L. V., R. W. Li, C. Li, J. M. Thomson, and B. J. Bequette. 2012. Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers. Physiol. Genomics 44:543-550. DOI ScienceOn |
15 | Cloonan, N. and S. M. Grimmond. 2008. Transcriptome content and dynamics at single-nucleotide resolution. Genome Biol. 9:234. DOI ScienceOn |
16 | de Hoon, M. J. L., S. Imoto, J. Nolan, and S. Miyano. 2004. Open source clustering software. Bioinformatics 20:1453-1454. DOI ScienceOn |
17 | Driver, A. M., F. Penagaricano, W. Huang, K. R. Ahmad, K. S. Hackbart, M. C. Wiltbank, and H. Khatib. 2012. RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts. BMC Genomics 13:118. DOI |
18 | He, H. and X. Liu. 2013. Characterization of transcriptional complexity during longissimus muscle development in bovines using high-throughput sequencing. PloS one 8(6):e64356. DOI |
19 | Livak, K. J. and T. D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25:402-408. DOI ScienceOn |
20 | Huang, D. W., B. T. Sherman, and R. A. Lempicki. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4:44-57. DOI |
21 | Trapnell, C., B. A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M. J. van Baren, S. L. Salzberg, B. J. Wold, and L. Pachter. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28:511-515. DOI ScienceOn |
22 | Hausman, G. J., M. V. Dodson, K. Ajuwon, M. Azain, K. M. Barnes, L. L. Guan, Z. Jiang, S. P. Poulos, R. D. Sainz, S. Smith et al. 2009. Board-invited review: the biology and regulation of preadipocytes and adipocytes in meat animals. J. Anim. Sci. 87:1218-1246. DOI ScienceOn |