Transcriptomics

Dataset Information

4

Aspergillus niger exposed to combinations of carbon source, nitrogen source, nitrogen concentration, and culture pH


ABSTRACT: Microarray analysis of Aspergillus niger under conditions with differing combinations of carbon source, nitrogen source, nitrogen concentration, and culture pH Fermentor cultures were grown in minimal medium (MM) at a constant temperature of 30 ± 0.5 ºC and with differing combinations of carbon source (either 277.5 mM glucose or 333.0 mM xylose), nitrogen source (NH4Cl or NaNO3) and nitrogen concentration (4x: 282.4 mM; 8x: 564.8 mM), and pH (pH4 or pH5) of the medium (M. Braaksma, A.K. Smilde, M.J. van der Werf, P.J. Punt, submitted for publication). At different time points samples were collected, quenched immediately in methanol at -45 ºC and centrifuged at -20 ºC to remove supernatant. Part of the biomass was frozen into liquid nitrogen and stored at -80 ºC for microarray analysis. For each of the 16 culture conditions one sample was selected for microarray analysis; samples were collected either around the time point carbon source depleted or a considerable time (~24 h) after carbon souce depletion. In addition some technical duplicates were included. 20 samples were analyzed from 16 different fermentation conditions. The fermentation conditions were varied according to a full factorial design of four factors tested at two levels. From one fermentation two different time samples were analyzed, from another fermentation four samples, two technical replicates of two different time samples, were analyzed. Samples were collected either around the time point carbon source depleted or a considerable time (~24 h) after carbon souce depletion.

ORGANISM(S): Aspergillus niger  

SUBMITTER: Machtelt Braaksma   Machtelt Braaksma  Peter J Punt  Mariët J Van der Werf  Trifa Omer 

PROVIDER: E-GEOD-17329 | ArrayExpress | 2010-04-08

SECONDARY ACCESSION(S): GSE17329PRJNA119011

REPOSITORIES: GEO, ArrayExpress

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Publications

Identification of modules in Aspergillus niger by gene co-expression network analysis.

van den Berg Robert A RA   Braaksma Machtelt M   van der Veen Douwe D   van der Werf Mariët J MJ   Punt Peter J PJ   van der Oost John J   de Graaff Leo H LH  

Fungal genetics and biology : FG & B 20100327 6


The fungus Aspergillus niger has been studied in considerable detail with respect to various industrial applications. Although its central metabolic pathways are established relatively well, the mechanisms that control the adaptation of its metabolism are understood rather poorly. In this study, clustering of co-expressed genes has been performed on the basis of DNA microarray data sets from two experimental approaches. In one approach, low amounts of inducer caused a relatively mild perturbatio  ...[more]

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