Transcriptomics,Genomics

Dataset Information

41

Transcriptome Profiling of Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola on two different medias


ABSTRACT: Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) are important bacterial pathogens of the worldwide staple and grass model, rice. Xoo invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice throughout the world. Xoc colonizes the parenchyma tissue to cause bacterial leaf steak, a disease of emerging importance. We have designed oligonucleotide probes (50-70-mers) represented 2,858 Xoo genes and 1,816 Xoc genes annotated by The Institute for Genomic Research (TIGR). To validate the Xo arrays, self-hybridization samples and tests of the non-specific hybridization using randomly spotted oligonucleotides corresponding to the hygromycin phosphotransferase gene (hph), and blank spot and of the correlation coefficient between biological replicates as well as between duplicate spots revealed that the data generated from our oligo array were highly reliable and consistent. To demonstrate application of Xo array, we performed expression profiling experiments on arrays hybridized with RNA of Xoo and Xoc grown in the two different nutrient-condition media. Several sets of genes involved in bacterial movement, chemotaxis, and hrp genes differentially express in response to different treatment. Due to comprehensive views of microarray study, extended biological events of plant-bacteria interaction was described. This publicly available microarray for Xanthomonas oryzae (Xo) is an enabling resource for a large and international community of scientists to better understand not only Xo biology but also many other Xanthomonas species that cause significant losses on crops. Keywords: Media condition response Overall design: Two different types of medias, PSB and XOM2, are used for culturing both Xoo and Xoc. 3 biological replicates and dye-swap replicates. 6 slides per experiment

INSTRUMENT(S): UCD_Ronald_XOarray_5K_V1.0

SUBMITTER: Malinee Sriariyanun  

PROVIDER: GSE9640 | GEO | 2008-02-08

SECONDARY ACCESSION(S): PRJNA105201

REPOSITORIES: GEO

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