Transcriptomics,Genomics

Dataset Information

21

Global changes of gene expression during scleroglucan synthesis in Sclerotium rolfsii


ABSTRACT: Two S. rolfsii transcriptomes obtained from scleroglucan-producing and scleroglucan-nonproducing conditions were pooled and sequenced using the 454 pyrosequencing technique yielding ~350,000 reads earlier. These could be assembled into 21,937 contigs and 171,833 singletons, for which 6,951 had significant matches in public protein data bases. Our first transcriptomic analysis, comparing an early stage of scleroglucan synthesis in high-level and low-level producing media, uncovered that most differentially expressed unigenes belong to the functional categories ‘metabolism’ and ‘transport’ (Schmid et al., 2010). In order to get more insights into transcriptional regulation of scleroglucan production, we extended in this study our transcriptomic analyses. We determined transcriptomic profiles for a later stage of cultivation in both media, thus giving us the opportunity to study temporal phenomena under high- and low-level producing conditions. Overall design: Tailor-made microarrays (44K multiplex chip, Agilent) were designed by imaGenes (Berlin, Germany) using an in-house developed method for empirical selection of best performing probes for each gene (Pre Selection Strategy). Briefly, up to ten probes were designed for each of the 454 unigenes (60 bp long oligomers). The 244K Agilent test array was hybridized with pooled Cy3-labeled cRNAs gained form EPSmax13 and EPSmin17 cultures and (in average) two of the best performing oligos were selected for each unigene. For comparative expression profiling, total RNA was isolated from S. rolfsii, cultured for 61 h in EPSmax13 (biological triplicate) and EPSmin17 media (biological triplicate). RNA quality control, synthesis of Cy3-labeled cRNA including cRNA purification and cRNA quality control, microarray hybridization, scanning and data extraction (Agilent´s feature extraction software) were performed by imaGenes GmbH. Expression data were analyzed by imaGenes GmbH using an in-house developed data analysis pipeline. After quantile normalization, genes were defined as differentially expressed if their expression levels varied at least 2 fold in EPSmax13 samples compared to EPSmin17 samples and if the difference was statistically significant (Student’s t-test, P-value cut-off of 0.05).

INSTRUMENT(S): Agilent-017067 Sclerotium rolfsii 44K multiplex chip, Agilent (Tailor-made microarrays, condensed version)

SUBMITTER: Jochen Schmid  

PROVIDER: GSE25254 | GEO | 2011-03-01

SECONDARY ACCESSION(S): PRJNA134679

REPOSITORIES: GEO

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Publications

Scleroglucan: biosynthesis, production and application of a versatile hydrocolloid.

Schmid Jochen J   Meyer Vera V   Sieber Volker V  

Applied microbiology and biotechnology 20110706 4


Since its first description in the early 1960s, scleroglucan attracted much attention from both academia and industry. Scleroglucan is an exopolysaccharide secreted by the basidiomycete Sclerotium rolfsii and appreciated as a multipurpose compound applicable in many industrial fields, including oil industry, food industry and pharmacy. In this review, the current knowledge on scleroglucan chemistry, genetics, biosynthesis and production will be summarized and different application possibilities  ...[more]

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