Project description:Chlorella sp. HS2 is a halotolerant microalga exhibiting relatively high biomass productivity and substantially high lipid accumulation in marine growth media, which suggests this alga as an important crop for industrial algal cultivation systems. To determine pathways leading to HS2's acclimation responses to salt stress, we performed RNA-seq analysis with triplicated cultures grown in freshwater and marine media at both exponential and stationary growth phases. We then run de novo assembly to obtain HS2 transcriptome, which in turn was annotated and processed to extract dysregulated pathways. Results showed a large proportion of down-regulated genes, for instance photosynthesis and TCA pathways. Photosynthesis appeared, however, to recover at the stationary phase, while the general down-regulation pattern was maintained.
Project description:We use untargeted high-resolution mass spectrometry to understand the metabolic differences at exponential and stationary growth stages using 22 Chlorella strains collected from South East Asia. Using this data, we demonstrate the use of a filtering procedure based on the SVD on the untargeted metabolite profile data, compared over two growth stages and run in four batches, and to remove structure in data related to day of sample assay. This approach preserves signal of demonstrable biological origin (strain-related variation in mass feature intensity) after minimizing the influence of batch effects. Our approach will be broadly applicable in metabolomics analysis to identify and remove batch effects. See MTBLS129 for associated study.
Project description:Proteomic data from E. coli grown with or without the azo dye, Red Dye number 40. WT and delta fnr E. coli were cultured in Luria Broth media and cultures were inoculated with 250 uM Red No. 40 at either mid-exponential or stationary growth phases. Vehicle control samples were also analyzed at mid-exponential and stationary growth phases.
Project description:The transition between exponential and stationary phase is a natural phenomenon for all bacteria and requires a massive readjustment of the bacterial transcriptome. Exoribonucleases are key enzymes in the transition between the two growth phases. PNPase, RNase R and RNase II are the major degradative exoribonucleases in Escherichia coli. We analysed the whole transcriptome of exponential and stationary phases from the WT and mutants lacking these exoribonucleases (Δpnp, Δrnr, Δrnb, and ΔrnbΔrnr). When comparing the cells from exponential phase with the cells from stationary phase more than 1000 transcripts were differentially expressed, but only 491 core transcripts were common to all strains. There were some differences in the number and transcripts affected depending on the strain, suggesting that exoribonucleases influence the transition between these two growth phases differently. Interestingly, we found that the double mutant RNase II/RNase R is similar to the RNase R single mutant in exponential phase while in stationary phase it seems to be closer to the RNase II single mutant. This is the first global transcriptomic work comparing the roles of exoribonucleases in the transition between exponential and stationary phase.
Project description:Genome-wide gene expression analysis was performed with the cells in exponential and stationary growth phases. Through these two growth status, 89.6% of currently annotated genes were expressed.
Project description:Identification of the specific SigA binding regions on the B. subtilis chromosome during exponential, transition and stationary growth phases. The data served to help the analysis of the repertoire of B. subtilis promoters established from transcriptome profiles. 3 growth phases (exponential, transition, stationary) x 2 biological replicates were analysed on the BsubT2 tiling array.
Project description:Identification of the specific SigA binding regions on the B. subtilis chromosome during exponential, transition and stationary growth phases. The data served to help the analysis of the repertoire of B. subtilis promoters established from transcriptome profiles. 3 growth phases (exponential, transition, stationary) x 2 biological replicates were analysed on the BsubT1 tiling array.
Project description:Identification of the specific SigA binding regions on the B. subtilis chromosome during exponential, transition and stationary growth phases. The data served to help the analysis of the repertoire of B. subtilis promoters established from transcriptome profiles.
Project description:Identification of the specific SigA binding regions on the B. subtilis chromosome during exponential, transition and stationary growth phases. The data served to help the analysis of the repertoire of B. subtilis promoters established from transcriptome profiles.
