Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression ATLAS of Oryza sativa sp japonica (cv. Nipponbare) during photomorphogenesis (transition from dark to light)

ABSTRACT: Oryza sativa Japonica (rice) is the staple food for all over world population. At the time of germination, the exposure to light may play an important role in the early development of the rice seedling. In order to survey the genes, their functions and role in biological processes, an RNA-Seq based study of 6 libraries prepared from poly-A rich mRNA fraction was carried out to explore transcriptional programs operating in dark and light conditions. For each treatment type, three individual plants were used as biological replicates.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Pankaj Jaiswal

PROVIDER: E-MTAB-5689 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most destructive bacterial disease of rice. The cloned rice gene Xa21 confers resistance to a broad spectrum of Xoo races. To identify other genes involved in Xa21-mediated immunity, a whole-genome oligonucleotide microarray of rice was used to profile the expression of rice genes between incompatible interactions and mock treatments at 0, 4, 8, 24, 72 and 120 hours post inoculation (hpi) or between incompatible and compatible interactions at 4 hpi, respectively. A total of 441 differentially expressed genes, designated as XDGs (Xa21 mediated Differentially expressed Genes), were identified. Based on their functional annotations, the XDGs were assigned to 14 categories some of which encode resistance/defense related proteins and signaling regulators. Interestingly, most signaling-related genes were down-regulated at 4 and 8 hpi, suggesting that negative regulation of cellular signaling may play a role in the Xa21-mediated defense response. Moreover, a number of pathogenesis-related genes were induced at 72 and 120 hpi. Comparison of expression profiles mediated by other resistance genes revealed an interesting common responses in the plant immune system. Comparison analyses also suggest possible overlaps with hormone signaling pathways and with defense systems including basal defense and hypersensitive responses. We investigated the transcriptional characteristics of Xa21-mediated defense responses in rice using whole-genome oligonucleotide microarray, by comparing the expression profiles between incompatible interactions and mock treatments at five time-points and between incompatible and compatible interactions at 4 hours post inoculation. Microarray hybridization at each time point was carried out in three replications including two biological replications and one technological replication. To detect the genes that are significantly regulated and to eliminate those that have inconsistent expression data among replicated experiments, a cutoff of 1.5 fold change and 1.96 for intensity-dependent Z-scores were required in at least two experimental samples.

Dataset Information

Gene expression ATLAS of Oryza sativa sp japonica (cv. Nipponbare) during photomorphogenesis (transition from dark to light)

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