Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Oryza sativa subtypes Cultivar Nagina-22 (N22) and IR64 subtypes under normal and drougth conditions.

ABSTRACT: High quality RNA was extracted from the whole seedlings (Combined root and leaf samples) using TRI Reagent (Ambion, Inc. USA) and pooled from 12 independent stressed and non-stressed plant samples separately, and treated with DNase-I (QIAGEN GmbH, Germany). Subsequently, RNA cleanup was carried out using RNeasy Plant Mini Kit (QIAGEN GmbH, Germany) and 5 ug of total RNA from each sample in triplicates were reverse-transcribed to double stranded cDNA using the GeneChipï¾® One-Cycle cDNA Synthesis Kit. The biotin-labelled cRNA was made using the GeneChipï¾® IVT Labelling Kit (Affymetrix, CA, USA). Twenty microgram of cRNA samples was fragmented and out of which which 7.5 ug cRNA were hybridized for 16 hours at 45C to the Affymetrix GeneChipï¾® Rice Genome Array (Santa Clara, CA, USA). After washing and staining with R-phycoerythrin streptavidin in a Fluidics Station, using the Genechipï¾® Fluidics Station 450, the arrays were scanned by the Genechipï¾® 3000 Scanner. The chip images were scanned and extracted using default settings and the CEL files were produced with the Affymetrix GeneChip Operating Software (GCOS 1.2). The resulting .CEL files were imported into the GeneSpring GX 10 (Agilent Technologies Inc, Santa Clara CA) and normalized with the PLIER16 algorithm. The resulting expression values were log2-transformed. Average log signal intensity values of three technical replicates for each sample were used for advance analysis.

ORGANISM(S): Oryza sativa Indica group

SUBMITTER: Sangram Lenka

PROVIDER: E-MEXP-2401 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance.

Lenka Sangram K SK Katiyar Amit A Chinnusamy Viswanathan V Bansal Kailash C KC

Plant biotechnology journal 20100831 3

Genetic improvement in drought tolerance in rice is the key to save water for sustainable agriculture. Drought tolerance is a complex trait and involves interplay of a vast array of genes. Several genotypes of rice have evolved features that impart tolerance to drought and other abiotic stresses. Comparative analysis of drought stress-responsive transcriptome between drought-tolerant (DT) landraces/genotypes and drought-sensitive modern rice cultivars will unravel novel genetic regulatory mechan ...[more]

PMID: 20809928

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Dataset Information

Transcription profiling of Oryza sativa subtypes Cultivar Nagina-22 (N22) and IR64 subtypes under normal and drougth conditions.

Publications

Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance.

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