Computational protocol: The antioxidative defense system is involved in the premature senescence in transgenic tobacco (Nicotiana tabacum NC89)

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Protocol publication

[…] The tobacco plants were grown under greenhouse conditions as described previously. Samples were collected from 8-week-old plants. To produce a transcriptome dataset with a wide coverage, RNA was extracted from pooled samples of leaves from four plants of WT and T3-2, respectively. The high-quality reads were assembled with the software package Velvet_1.2.10. The trimmed Solexa transcriptome reads were mapped onto the unique consensus sequences using Bowtie. Unigenes were compared to records in public databases, including the National Center for Biotechnology Information (NCBI, 2013), SWISS-PROT, kyoto encyclopedia of genes and genomes database (KEGG), and gene ontology (GO). Transcriptome sequencing was performed by Capital Bio Corporation (Beijing, China), using Hiseq 2000. [...] Statistical analyses were performed using SigmaPlot 12.0 software, Excel, and data processing system (DPS) procedures (Zhejiang University, Zhejiang, China). Differences among means were compared using Tukey’s multiple range test at a 0.05 probability level. […]

Pipeline specifications

Software tools Velvet, Bowtie, SigmaPlot
Databases UniProt KEGG
Applications Miscellaneous, RNA-seq analysis
Organisms Nicotiana tabacum, Malus domestica
Diseases Machado-Joseph Disease
Chemicals Hydrogen Peroxide, Mevalonic Acid, Nitrogen, Oxygen, Superoxides