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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression analysis of various fungi grown in glucose or xylose

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE24853: Expression analysis of Spathaspora passalidarum NRRL Y-27907 grown in glucose or xylose GSE24854: Expression analysis of Pichia stipitis CBS 6054 grown in glucose or xylose GSE24855: Expression analysis of Lodderomyces elongisporus NRRL YB-4239 grown in glucose or xylose GSE24856: Expression analysis of Candida tenuis NRRL Y-1498 grown in glucose or xylose GSE24857: Expression analysis of Candida albicans WO-1 grown in glucose or xylose Refer to individual Series

ORGANISM(S): Candida albicans WO-1

SUBMITTER: Dana Wohlbach

PROVIDER: E-GEOD-24858 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression analysis of Spathaspora passalidarum NRRL Y-27907 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Spathaspora passalidarum NRRL Y-27907 grown aerobically in xylose, compared to the same strain grown aerobically in glucose. A six array study using total RNA recovered from three separate cultures of Spathaspora passalidarum NRRL Y-27907 grown in glucose and three separate cultures of Spathaspora passalidarum NRRL Y-27907 grown in xylose. Each array measures the expression level of 362,487 probes (average probe length 54.5 +/- 4.0 nt) tiled across the Spathaspora passalidarum NRRL Y-27907 genome with a median spacing distance of 29 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.

2011-10-19 | E-GEOD-24853 | biostudies-arrayexpress

Expression analysis of Candida albicans WO-1 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Candida albicans WO-1 grown aerobically in xylose, compared to the same strain grown aerobically in glucose. A six array study using total RNA recovered from three separate cultures of Candida albicans WO-1 grown in glucose and three separate cultures of Candida albicans WO-1 grown in xylose. Each array measures the expression level of 373,067 probes (average probe length 55.2 +/- 4.0 nt) tiled across the Candida albicans WO-1 genome with a median spacing distance of 31 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.

2011-10-19 | E-GEOD-24857 | biostudies-arrayexpress

Expression analysis of Candida tenuis NRRL Y-1498 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Candida tenuis NRRL Y-1498 grown aerobically in xylose, compared to the same strain grown aerobically in glucose. A six array study using total RNA recovered from three separate cultures of Candida tenuis NRRL Y-1498 grown in glucose and three separate cultures of Candida tenuis NRRL Y-1498 grown in xylose. Each array measures the expression level of 363,196 probes (average probe length 53.1 +/- 3.8 nt) tiled across the Candida tenuis NRRL Y-1498 genome with a median spacing distance of 24 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.

2011-10-19 | E-GEOD-24856 | biostudies-arrayexpress

Expression analysis of Pichia stipitis CBS 6054 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Pichia stipitis CBS 6054 grown aerobically in xylose, compared to the same strain grown aerobically in glucose. A six array study using total RNA recovered from three separate cultures of Pichia stipitis CBS 6054 grown in glucose and three separate cultures of Pichia stipitis CBS 6054 grown in xylose. Each array measures the expression level of 374,100 probes (average probe length 53.6 +/- 4.1 nt) tiled across the Pichia stipitis CBS 6054 genome with a median spacing distance of 33 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.

2011-10-19 | E-GEOD-24854 | biostudies-arrayexpress

Expression analysis of Lodderomyces elongisporus NRRL YB-4239 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Lodderomyces elongisporus NRRL YB-4239 grown aerobically in xylose, compared to the same strain grown aerobically in glucose. A six array study using total RNA recovered from three separate cultures of Lodderomyces elongisporus NRRL YB-4239 grown in glucose and three separate cultures of Lodderomyces elongisporus NRRL YB-4239 grown in xylose. Each array measures the expression level of 371,451 probes (average probe length 54.1 +/- 4.1 nt) tiled across the Lodderomyces elongisporus NRRL YB-4239 genome with a median spacing distance of 33 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.

2011-10-19 | E-GEOD-24855 | biostudies-arrayexpress

Array competitive genomic hybridization of three Saccharomyces cerevisiae strains vs. DBY8268

Project description:A six array study using total gDNA recovered from two separate cultures of each of three different strains of Saccharomyces cerevisiae (YB-210 or CRB, Y389 or MUSH, and Y2209 or LEP) and two separate cultures of Saccharomyces cerevisiae DBY8268. Each array measures the hybridization of probes tiled across the Saccharomyces cerevisiae genome. Biological replicates: 2 for each strain, 2 for control. Grown and harvested in parallel. One replicate per array.

2014-10-01 | E-GEOD-56441 | biostudies-arrayexpress

Comparative xylose metabolism among the ascomycetes C. albicans, S. stipitis and S. cerevisiae

Project description:The ascomycetes Saccharomyces cerevisiae, Candida albicans and Scheffersomyces stipitis metabolize the pentose sugar xylose very differently. S. cerevisiae fails to grow on xylose, while C. albicans can grow, and S. stipitis can both grow and ferment xylose to ethanol. However, all three species contain highly similar genes that encode xylose reductase and xylitol dehydrogenase required to convert xylose to xylulose, on which all three fungi grow. We have created C. albicans strains deleted for either or both the xylose reductase gene GRE3, and the xylitol dehydrogenase gene XYL2. As expected, all the mutant strains cannot grow on xylose, while the gre3 mutant can grow on xylitol. The gre3 and xyl2 mutants are complemented efficiently by the XYL1 and XYL2 from S. stipitis respectively. Intriguingly, the S. cerevisiae GRE3 and SOR1 genes can complement the gre3 and xyl2 mutants respectively, showing that S. cerevisiae contains the enzymatic capacity for converting xylose to xylulose. In addition, the gre3 xyl2 double mutant is effectively rescued by the xylose isomerase (XI) gene of either Piromyces or Orpinomyces, suggesting that the XI provides an alternative to the missing oxido-reductase functions in the mutant required for the xylose-xylulose conversion. Overall this work establishes that C. albicans strains engineered to lack essential steps for xylose metabolism provide a platform for the analysis of xylose metabolism enzymes from a variety of species, and confirms that S. cerevisiae has the genetic potential to convert xylose to xylulose, although non-engineered strains cannot proliferate on xylose as the sole carbon source. Transcription profile of cells in xylose compared to glucose. Two sets: Candida albicans, 1 condition ; Saccharomyces cerevisiae 2 conditions / in xylose (SX) or no sugar (S) (replicates with dye-swap)

2013-10-30 | E-GEOD-50476 | biostudies-arrayexpress

Xylose metabolism in Candida utilis

Project description:A recombinant C. utilis strain expressing Candida shehatae xylose reductase K275R/N277D (NADH-preferring), C. shehatae xylitol dehydrogenase and Pichia stipitis xylulokinase produce ethanol from xylose. Here, we report the transcriptional-profiling in the engineered C. utilis strain grown on xylose using DNA microarray. Transcriptome analysis indicated that expression of genes encoding the tricarboxylic acid cycle, respiration enzymes and the ethanol consumption were increased significantly when cells were cultivated on xylose. Gene expression in Candida utilis cells grown on glucose or xylose was measured at 10.5 and 24 hours, respectively. Two or three independent experiments were performed at each time for each experiment.

2014-01-01 | E-GEOD-43514 | biostudies-arrayexpress

Transcription profiling of S. cerevisiae xylose metabolism mutants grown on glucose and xylose under aerobic and anaerobic conditions

Project description:Response of Saccharomyces cerevisiae engineered for xylose metabolism to changes in carbon source and aeration

2007-07-07 | E-GEOD-835 | biostudies-arrayexpress

Genome wide expression analysis of genes regulated by SGE1 in Fusarium verticillioides

Project description:Investigation of whole genome expression changes induced by SGE1 30 minutes after induction of SGE1 expression in an SGE1 mutant strain of Fusarium verticillioides. Comparison between wild-type, SGE1 overexpression mutant GMTcp-272 (xlnp:SGE1 in SGE1 mutant background) and sge1 mutant in liquid medium (18 hrs) after induction with xylose. SGE1 plays a role in pathogenicity and synthesis of secondary metabolism. In this study, total RNA recovered from nine cultures of F. verticillioides (wild-type, sge1 mutant and SGE1 overexpression mutant GMTcp-272, in triplicate) 30 minutes after the addition of xylose was used to identify genes regulated by SGE1.

2014-04-09 | E-GEOD-56664 | biostudies-arrayexpress

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