Arabidopsis transcriptional profile in response to chromate (K2CrO4)
ABSTRACT: Transcriptional profiling of Arabidopsis thalina seedlings in response to high (140 µM) and low (20 µM) concentrations of chromate (K2CrO4). Low concentrations of chromate (e.g. 40 µM) promoted primary root growth, while high concentrations (e.g. 140 µM) repressed growth and increased formation of root hairs, lateral roots and adventitious roots. Three-condition experiment, high (140 µM) and low (20 µM) concentrations of chromate (K2CrO4) vs non-chromate added (Control). Four biological replicates, one replicate per array.
Project description:Transcriptional profiling of three mexican maize landraces under 10, and 17 days stress and recovery irrigation A dye balanced modified loop design was implemented. Two biological replicates (pooling five representative plants) representing each sampling point for each genotype were obtained for purified RNA from 120 randomly chosen seedlings. This experiment involved a total of forty-eight (24 sets) of microarray hybridizations, including direct and dye swap comparisons between treatments as well as across the three landraces. This design allowed us to determine differences in gene expression between the three different landraces under drought stress (10 and 17 days) and at recovery irrigation compared to irrigated controls.
Project description:Transcriptional profiling of 6 days-old Arabidopsis thaliana Col-0 seedlings transfered to alkamide decanamide-containing medium in a 1, 3, 7 and 14 d time course period. Keywords: Pharmacological A dye balanced modified loop design was implemented. Four biological replicates representing each sampling point were obtained by pooling in a 1:1 proportion shoot and root purified RNA from 120 randomly chosen seedlings. This experiment involved a total of sixteen sets of microarray hybridizations, including direct and dye swap comparisons between treatments as well as across time points for the same treatment. This design allowed us to determine differences in gene expression between N-isobutyl decanamide-treated and control seedlings, and whether the differences were time dependent.
Project description:Five members of the Arabidopsis thaliana NF-YA gene family are strongly induced by several stress conditions via transcriptional and miR169-related posttranscriptional mechanisms. These transcription factors participate in gene regulation via two different mechanisms, one depending on binding to the CCAAT-box in the promoter of regulated genes and the other, independent of the CCAAT-box, in which NF-YA prevents the interaction of the NF-YB/YC heterodimer with transcription factors. Three biological and two technical (in swap) replicates for each genotype were obtained for each treatment (DMSO (mock) and estradiol 24h after induction). Mock samples were pooled and used as a reference.
Project description:Transcriptional profiling of roots from 12 days-old Arabidopsis thaliana seedlings transfered to Pi-deficient medium in hydroponic solution in a 10 min, 30 min, and 2 hrs time course period. A dye balanced modified loop design was implemented. This experiment involved a total of twelve sets of microarray hybridizations, including direct and dye swap comparisons between treatments as well as across time points for the same treatment. This design allowed us to determine differences in gene expression between Pi-deprived and control seedlings, and whether the differences were time dependent. Four biological replicates representing each sampling point were obtained.
Project description:Arabidopsis thaliana Col-0 plants and three other genotypes (ARR1 overexpressor, arr1-1 knockout, overexpressor of ARR1-SRDX fusion protein) were grown in liquid media (1/2 MS, 1 g/L sucrose, 0.5 g/L MES, pH 5.7) in a Percival AR-66L growth chamber at 24 oC, 16:8 h day:night cycle, and 100 µE light intensity until growth stage 1.0. Plants were then treated with 5 µM 6-Benzyladenine for 0, 15, and 120 min, harvested and frozen in liquid nitrogen for RNA extraction and subsequent processing for microarray hybridization.
Project description:cDNA macroarray expression profiling was carried out in poplar roots in order to identify genes regulated in response to exposition to copper stress. For this purpose, plants of a Populus deltoides clone grown in a hydroponic system during four weeks were incubated in a nutrient solution (Hoagland's modiefied salt, ¼ strength) supplemented with copper (0 µM (control), 30 µM and 60 µM). Roots were sampled at 12 and 24 h after exposition in a time-course experiment. Three biological replicates named Rep1, Rep2 and Rep3 were obtained for each copper treatment (i.e., control, Cu30 and Cu60) at each time point (i.e., 12, 24). At each time point, two comparisons were performed: control treatment versus Cu30 and control treatment versus Cu60. For each comparison, biological triplicates were used to identify transcripts differentially regulated at the considered timepoint using a statistical analysis approach based on linear mixed models by the SAS system.
Project description:Legumes, in interaction with resistant rhizobia, combined both moderate tolerance and accumulation of metal(loids) in roots, with the ability to grow without nitrogen supply (Pajuelo et al., 2011). This quality has attracted attention for phytostabilisation of polluted soils (Reichman, 2007). Physiological studies suggest that low arsenite concentrations lead to a decrease of nodulation process (Dary et al., 2010; Pajuelo et al., 2008). Moreover, Lafuente et al. (2010) described a reduction in the expression patterns of nodulins genes in the presence of arsenite. Nevertheless, a global transcriptomic analysis has never been approached. In order to decipher the genetic regulation underlying the arsenite effect on the model symbiotic interaction Medicago-Sinorhizobium, we have performed a meta-analysis of three different hybridizations. These compare transcriptomic profiles of roots cultivated under different treatments (±25 µM arsenite, ±rhizobia).