Project description:An updated representation of S. meliloti metabolism that was manually-curated and encompasses information from 240 literature sources, which includes transposon-sequencing (Tn-seq) data and Phenotype MicroArray data for wild-type and mutant strains.
Project description:The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p is an atypical La motif containing protein (LARP). LARPs are members of a superfamily of RNA-binding proteins conserved across eukaryotes. Transcriptomics and RIP-Seq analysis suggested an effect of Slf1 on the amount of mRNA of genes involved in the response to oxidative stress. To quantify these effects at the protein level, we used label-free mass spectrometry to compare the proteomes of wild-type and slf1Δ mutant strains following oxidative stress conditions. This analysis identified several proteins which are normally induced in response to hydrogen peroxide, but where this increase is attenuated in the slf1Δ mutant.
Project description:ra06-03_dspa-erwinia - dspa/e of erwinia amylovora - Identification of Arabidopsis genes regulated by the type three effector Dspa/E of Erwinia amylovora. - Regulation of the Arabidopsis transcriptome by the type three effector DspA/E of Erwinia amylovora. 5-week old Arabidopsis plants were leaf infiltrated with Erwinia amylovora wild-type (wt), type three secretion mutant (sec) or dspA/E mutant (dspA/E) strains. Keywords: wt vs mutant comparison
Project description:AtR8 is a long non-coding RNA transcribed by RNA polymerase III in Arabidopsis which is responsive to hypoxic stress and salicylic acid. To understand the role of AtR8 lncRNA, microarray was carried out in the mutant seedlings of AtR8 and compared with wild type seedlings.
Project description:AGO4 plays an important role in RNA-directed DNA methylation (RdDM). RdDM on specific genomic loci have the potential to silence the nearby protein coding gene. We used wild-type La-er and ago4-1 mutant Arabidopsis to identify AGO4-regulated genes.
Project description:To investigate the role of Sir2 controlling gene expression during U. maydis pathogenesis, sir2 was deleted and overexpressed with Ppit2 promoter. RNA-Seq analysis were performed during axenic growth or filament formation in PD-Charcoal plates comparing Δsir2 mutan and wild type strains. Additionally RNA-Seq analysis were performed at 3 days post infection comparing Ppit2:sir2 >1c overexpression mutant and wild type strains.
Project description:The aim of this study was to perform a transcriptional characterization of the Arabidopsis eds4 mutant. To this end two separate experiments were performed: Experiment 1: comparison of the transcriptional profile (RNA-seq) of eds4 Arabidopsis mutants in contrast to wild type Col-0 accession grown under continuous light conditions. Experiment 2: Analysis of the distribution of transcripts (RNA-seq) between nucleus and cytoplasm in the eds4 Arabidopsis mutants in comparison to wild type Col-0 plants grown under continuous light conditions.
Project description:<p>Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12Ac ChIP-seq data for wild-type and mip6delta strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress.</p>