Project description:Expression profiling of A. thaliana, A. stelleri, R. islandica, and T. salsuginea under the low-oxygen treatment(0.1% O2/99.9% N2, various time points at 0, 1, 3, 8, 24, 72h) Comparative analysis of transcriptional responses to low-oxygen stress with Arabidopsis and its related species to gain comprehensive insights into low-oxygen responses of the species.
Project description:In the present work we report data on the application of an integrated approach on apples held under two levels of low oxygen concentrations throughout the initial 2 months of storage, when, in general, strict control of the effects of the extremely low oxygen concentration is required for a successful DCA performance.
Project description:In order to understand how Pseudomonas aeruginosa responds to low oxygen we grew strain PAO1 with 3 different oxygen concentrations: 2%, 0.4% and 0% supplemented with nitrate as an electron acceptor. Gene expression under these conditions was compared to that of cells grown with 20% oxygen. Keywords: Comparison of transcriptome profiles
Project description:In the present work we report data on the application of an integrated approach on apples held under two levels of low oxygen concentrations throughout the initial 2 months of storage, when, in general, strict control of the effects of the extremely low oxygen concentration is required for a successful DCA performance. Examination of 4 different condition. Three replicates per condition
Project description:Low-oxygen stress associated with natural phenomena such as waterlogging, results in widespread transcriptome changes and a metabolic switch from aerobic respiration to anaerobic fermentation. High-throughput sequencing of small RNA libraries obtained from low-oxygen stressed and control root tissue identified a total of 65 unique microRNA (miRNA) sequences from 46 families, and 14 trans-acting small interfering RNA (tasiRNA) from 3 families. Low-oxygen stress resulted in changes to the abundance of 46 miRNAs from 19 families, and all 3 tasiRNA families. Chemical inhibition of mitochondrial respiration caused similar changes in expression in a majority of the low-oxygen responsive small RNAs analysed. Our data indicate that miRNAs and tasiRNAs play a role in gene regulation and possibly developmental responses to low oxygen, and that a major signal for these responses is likely to be dependent on mitochondrial function. Keywords: Small RNA transcriptome analysis
Project description:Low-oxygen stress associated with natural phenomena such as waterlogging, results in widespread transcriptome changes and a metabolic switch from aerobic respiration to anaerobic fermentation. High-throughput sequencing of small RNA libraries obtained from low-oxygen stressed and control root tissue identified a total of 65 unique microRNA (miRNA) sequences from 46 families, and 14 trans-acting small interfering RNA (tasiRNA) from 3 families. Low-oxygen stress resulted in changes to the abundance of 46 miRNAs from 19 families, and all 3 tasiRNA families. Chemical inhibition of mitochondrial respiration caused similar changes in expression in a majority of the low-oxygen responsive small RNAs analysed. Our data indicate that miRNAs and tasiRNAs play a role in gene regulation and possibly developmental responses to low oxygen, and that a major signal for these responses is likely to be dependent on mitochondrial function. Keywords: Small RNA transcriptome analysis Examination of root tissue under 2 different environments, control and low oxygen
Project description:Comparison of stop1-mutant vs. wild type (WT;Col-0) treated with low-oxygen stress, and gene expression responses to low-oxygen in Arabidopsis shoots. Biological replicates: 3 replicates of shoot sample.
Project description:Environmental stresses trigger distinct responses between stress-sensitive and stress-adapted plants. To explore these stress adaptations at the cellular level, we built root single-cell transcriptome atlases for five biodiverse Brassicaceae species, including two stress-sensitive models (Arabidopsis thaliana and Sisymbrium irio), two extremophytes (Eutrema salsugineum and Schrenkiella parvula), and a polyploid oil crop (Camelina sativa), under control, salt, and ABA treatments. Although these species share similar root anatomy, most Arabidopsis cell type markers were not conserved across species. Cortex cell populations with distinct transcriptomes were spatially segregated among species. Lineage-specific gains in stress responses were more common than losses among cell-type responses across species. The homeologs in the allohexaploid C. sativa showed stress response divergence that was often decoupled from the divergence in their coding sequences and control expression levels. Our dataset provides a foundational root atlas across multiple Brassicaceae species enhanced for user accessibility with a cross species searchable browser and provides an analytical framework for comparative single-cell transcriptomics that can be readily transferred to any multi-species system.