Unknown,Transcriptomics,Genomics,Proteomics

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RNAseq analysis of Xcc strain B100 in minimum media

ABSTRACT: The dataset is a total transcriptome. RNA samples were obtained from fermentation of the Xcc strain B100 in minimal media named XMD (Schatschneider et al., 2013) with 30 g/L glucose as a sole carbon source and 0.4 g/L KNO3 as the sole nitrogen source . the RNA probes were harvested in the middle of the growth phase at an OD = 1 and the library was prepared following the protcol published by Pfeifer-Sancar et al., 2013.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Xanthomonas campestris pv. campestris

SUBMITTER: Daniel Wibberg

PROVIDER: E-MTAB-5578 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Transcriptome analyses using a wild-type strain of Saccharomyces cerevisiae were performed to assess the overall pattern of gene expression during the transition from glucose-based fermentative to glycerol-based respiratory growth. These experiments revealed a complex suite of metabolic and structural changes associated with the adaptation process. Alterations in gene expression leading to remodeling of various membrane transport systems and the cortical actin cytoskeleton were observed. Transition to respiratory growth was accompanied by alterations in transcript patterns demonstrating not only a general stress response, as seen in earlier studies, but also the oxidative and osmotic stress responses. In some contrast to earlier studies, these experiments identified modulation of expression for many genes specifying transcription factors during the transition to glycerol-based growth. Importantly and unexpectedly, an ordered series of changes was seen in transcript levels from genes encoding components of the TFIID, SAGA (Spt-Ada-Gcn5-Acetyltransferase), and SLIK (Saga LIKe) complexes and all three RNA polymerases, suggesting a modulation of structure for the basal transcriptional machinery during adaptation to respiratory growth. In concert with data given in earlier studies, the results presented here highlight important aspects of metabolic and other adaptations to respiratory growth in yeast that are common to utilization of multiple carbon sources. Importantly, they also identify aspects specific to adaptation of this organism to growth on glycerol as sole carbon source. A time-series illustrating the transition from fermentation using glucose (dextrose) as sole carbon source to respiration using glycerol as sole carbon source. Time points of 15 minutes, 30 minutes and 60 minutes as well as growth on dextrose, glycerol or ethanol as sole carbon source from a starter culture. Three biological replicates of the 30 minute time point and growth on glycerol from starter culture.

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RNAseq analysis of Xcc strain B100 in minimum media

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