Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of xylose metabolism in the methylotrophic yeast Hansenula polymopha

ABSTRACT: The transcriptomes of H. polymorpha grown on xylose were compared with those of glucose-grown cells under both aerobic and microaerobic conditions The transcriptomes of H. polymorpha grown on xylose were compared with those of glucose-grown cells under both aerobic and microaerobic conditions

ORGANISM(S): Ogataea angusta

SUBMITTER: Oh Cheol Kim

PROVIDER: E-GEOD-43240 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis of xylose metabolism in the methylotrophic yeast Hansenula polymopha

Project description:The transcriptomes of H. polymorpha grown on xylose were compared with those of glucose-grown cells under both aerobic and microaerobic conditions

2016-01-01 | GSE43240 | GEO

Transcription profiling Saccharomyces cerevisiae xylose metabolism

Project description:In the present study transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at genome-wide level how signalling and carbon catabolite repression differed in cells grown on either glucose or xylose. The more detailed knowledge about is xylose sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is it rather recognised as a non-fermentable carbon source is important in achieving understanding for further engineering this yeast for more efficient anaerobic fermentation of xylose. Experiment Overall Design: Three aerobic batch fermentations were carried out both on 50 g l-1 glucose and on 50 g l-1 xylose to compare the yeast transcriptome and proteome of cells growing on xylose with that of glucose repressed and glucose derepressed cells. Samples of the xylose-grown cells were harvested at 72 h from the start of the xylose cultures with 32 g l-1 of residual xylose present. Samples of the glucose repressed cells were harvested at 5 h from the start of the glucose cultures with 37 g l-1 of residual glucose present. Samples of the glucose derepressed cells were harvested at 24 h from the start of the glucose cultures containing no glucose but 13 g l-1 of accumulated ethanol.

2008-10-26 | E-GEOD-12890 | biostudies-arrayexpress

Xylose metabolism in recombinant Saccharomyces cerevisiae

2008-09-24 | GSE12890 | GEO

Transcription profiling of Aspergillus niger wild type and inuR deletion strains grown in sucrose and/or xylose to identify genes that are involved in inulin and sucrose metabolism

Project description:Microarray experiments were performed for identifying genes that are involved in inulin and sucrose metabolism by analyzing the transcriptomes of wild type strain N402 and inuR deletion strain grown in sucrose, as well as by analyzing the transcriptomes of wild type strain N402 grown in sucrose and xylose.

2008-06-01 | E-TABM-319 | biostudies-arrayexpress

Transcription profiling of Aspergillus niger amyR and wild type strains grown in maltose and xylose

Project description:Microarray experiments were performed for identifying genes that are involved in starch metabolism by analyzing the transcriptomes of wild type strain N402 and amyR deletion strain grown in maltose, as well as by analyzing the transcriptomes of wild type strain N402 grown in maltose and xylose.

2008-06-01 | E-TABM-324 | biostudies-arrayexpress

Transcriptome profile of wild type Azoarcus sp. BH72 grown under microaerobic condition (0.3% oxygen) compared with that grown under aerobic condition (21% oxygen), both in presence of combined nitrogen source, respectively

Project description:Low oxygen tensions are often encountered in flooded soils of rice fields by root-associated, strictly respiratory, beta proteobacterium, Azoarcus sp. BH72 which fixes nitrogen only under microaerobic condition. In this study, genome wide oligonucleotide microarrays were used compare the global transcription profile of Azoarcus sp. BH72 under microaerobic condition with cells grown under aerobic condition, both with ammonia as sole nitrogen source. The outcome of this study will provide a better insight about the establishment of this endophyte in the microaerobic environment, probably prevailing inside of the rice root niche .

2014-09-13 | GSE61387 | GEO

2014-09-13 | E-GEOD-61387 | biostudies-arrayexpress

Sugar-dependent gene expression in xylose grown A. thaliana cell suspension culture

Project description:Sugars modulate expression of hundreds of genes in plants. Previous studies on sugar signaling, using intact plants or plant tissues, were hampered by tissue heterogeneity, uneven sugar transport and/or inter-conversions of the applied sugars. This, in turn, could obscure the identity of a specific sugar that acts as a signal affecting expression of given gene in a given tissue or cell-type. To bypass those biases, we have developed a novel biological system, based on stem-cell-like Arabidopsis suspension culture. The cells were grown in a hormone-free medium and were sustained on xylose as the only carbon source. The functional genomics approach was used to identify sugar responsive genes, which rapidly (within 1 h) respond specifically to low concentration (1 mM) of glucose, fructose and/or sucrose. A habituated A. thaliana cell culture grown in a hormone free full strength MS media in the dark was adapted to growth on xylose as the only carbon source in the media.The cells were subjected to a 1 hour treatment with 1 mM of either Fru, Glc, Suc or Xyl (control). The experiments were carried out in 3 biological repeats per treatment. Whole genome expression analysis was conducted by hybridization of the extracted RNA to the Affymetrix Arabidopsis ATH1 Genome Array.

2014-05-16 | E-GEOD-57751 | biostudies-arrayexpress

Expression analysis of various fungi grown in glucose or xylose

Project description: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

2011-10-19 | E-GEOD-24858 | biostudies-arrayexpress

Impact of xylose feeding on transcriptome profiles of anaerobically fed-batch xylodextrins consumption in Saccharomyces cerevisiae

Project description:Saccharomyces cerevisiae cannot metabolize xylodextrins in nature. One engineered S. cerevisiae strain, which expresses XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, and cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. crassa, can utilize xylodextrins in aerobic condtions but not anaerobic conditions. We sequenced mRNA from anaerobically fed-batch cultures of the engineered S. cerevisiae grown on xylodextrins with or without the continuous feeding of xylose in biological duplicate. Dynamic changes of gene expression during xylose feeding experiment revealed by RNA deep sequencing indicated that xylose helps anaerobically xylodextrin-grown cells to recover mithondrial function thereby resuming xylodextrin consumption. Furthermore, different portions of genes involved in ribosome biogenesis showed either decreased or increased transcriptions. The underlying mechanism remains to be elucidated.

2021-05-27 | GSE69448 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data