The development of a RNA-sequencing pipeline based on tuxedo tools. Martijn Derks Masoed Ramuz Nick Alberts Rico Hagelaar. Index . Dataset Pipeline 1 ( Tophat_cuff ) Pipeline 2 ( Cuff_diff ) Pipeline 3 (Summary) Conclusions Future prospects. Dataset.
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based on tuxedo tools
Ganet al. 2011. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature. 477, P 419–423.
Input data (FastQ)Tophat_cuff
Total intron length
Basic for plot R
Control vs condition
Functions + enrichment
GC genes vs FPKM
CV= STDEV/ Average
Abscisic acid biosynthesis (stress conditions)
1. Cold, salinity and drought stresses: An overview
2. Cold stress regulation of gene expression in plants
ViswanathanChinnusamy et al.
Seki, M. Narusaka, M. Ishida, J. Nanjo, T. Fujita, M. Oono, Y. Kamiya, A. Nakajima, M. Enju, A. Sakurai, T. Satou, M. Akiyama, K. Taji, T. Yamaguchi-Shinozaki, K. Carninci, P. Kawai, J. Hayashizaki, Y. Shinozaki, K. 2002. Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. V 31. I 3. pp 279-292.
Baniwal, K. S. Bharti, K. Yu Chan, K. Fauth, M. Ganguli, A. Kotak, S. Mishra, S. K. Nover, L. Port, M. Scharf, K. Tripp, J. Weber, C. Zielinski, D. Koskull-Doring, P. 2004. Heat stress response in plants: a complex game with chaperones and more than twenty heat stress transcription factors. J Biosci. V 29. I 4. pp471-487.
Bartels, D. Nelson, D. 1994. Approaches to improve stress tolerance using molecular genetics. Plant, Cell and Environment. V 17. pp 659-667.
Wang, W. Vinocur, B. Shoseyov, O. Altman, A. 2004. Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. V 9. I 5. pp. 244-252.