Project description:This study profiles transcriptomic changes of Arabidopsis thaliana Col-0 in response to submergence. This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls from total mRNA populations of plants at 9 to 10 leaf rosette stage. Biological replicates of root and shoot tissues were harvested after 7 h and 24 h of submergence in darkness along with corresponding non-submerged dark controls. To characterize the dark response, non-submerged light controls plants were harvested at the 0 h time point. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform. Changes in the transcriptome in response to submergence and early darkness were evaluated, and the data led to identification of genes co-regulated at the conditional and organ-specific level.
Project description:RNA-seq profiling on the shoot and root tissues of Arabidopsis thaliana seedlings 7 day post inoculation with the plant growth promoting rhizobacteria (PGPR) Pseudomonas simiae WCS417r
Project description:Comparison of TopHat alignments and assessment of spurious splice junctions for 32nt and 76nt read lengths. Total RNA from 2-week-old Arabidopsis thaliana (ecotype Columbia) seedlings grown on MS plates was isolated using RNeasy Plant Mini Kit from Qiagen. To remove any contaminating DNA, RNA was treated with DNAse. Isolation of poly (A) mRNA and preparation of cDNA library were carried out using the Illumina TrueSeq RNA kit. Sequencing (72 cycle) was done on Illumina Genome Analyzer II.
Project description:Magnesium (Mg) is essential for many biological processes in plant cells and its deficiency causes yield reduction in crop systems. Low Mg status reportedly impacts on photosynthesis, sucrose partitioning and biomass allocation. However, earlier responses to Mg deficiency are scarcely described. Generally, symptoms of nutrient deficiency appear in specific ages of leaves. Therefore, we hypothesised that transcriptional responses to Mg deficiency are different depending on the ages of leaves, and performed a global transcriptomic analysis in two types of leaves; source and sink leaves of the model plant species Arabidopsis thaliana to reveal the earlier responses to Mg deficiency. The global transcriptomic study revealed that short-term Mg deficiency triggers the expression of defence response genes in sink leaves. In roots, although short-term Mg deficiency enhanced the Mg2+ uptake from the environmnet, transcriptional levels of genes encoding putative Mg2+ transporters in roots were unchanged, suggesting non-transcriptional regulation of Mg2+ uptake in roots.