GEO DataSets

(Submitter supplied) Aspergillus niger is a filamentous ascomycete fungus that is commonly found in most biotopes around the globe. In nature, A. niger degrades the plant biomass polysaccharides to monomeric sugars, transports them into the cells, and uses a variety of catabolic pathways to convert them into biochemical building blocks and energy. We show that when grown in liquid cultures, A. niger takes up plant-biomass derived monomeric sugars (and maltose) in a highly sequential manner, rather than simultaneously. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

8 Samples

Download data: CEL

(Submitter supplied) In this study, we compared the gene expression pattern of A. niger grown in liquid sugar beet pulp (SBP) at different time points, a by-product of the sugar industry that consists mainly of cellulose, xyloglucan, and pectin. Finally, we compared A. niger genetic response to liquid SBP to that of the same fungus when grown on solid SBP plates and polygalacturonic acid (PGA).

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL6758

8 Samples

Download data: CEL, TXT

(Submitter supplied) Plant biomass is the most abundant and renewable carbon source for many fungal species. The composition of biomass consists of about 40-45% cellulose, 20-30% hemicellulose, and 15-25% lignin and varies among plant species. In the bio-based industry, Aspergillus species and other fungi are used for the production of lignocellulolytic enzymes to pretreat agricultural waste biomass (e.g. wheat bran). In this study, we aimed to evaluate if it would be possible to create an Aspergillus strain that releases but does not metabolize hexoses from plant biomass. more...

Organism:

Aspergillus nidulans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19470

8 Samples

Download data: XLS

(Submitter supplied) Filamentous fungi are ubiquitous organisms and major plant biomass degraders. As a single colony, some fungal species can colonize large areas as up to five soccer stadia. During growth, the mycelium encounters heterogeneous carbon sources. Here we assessed whether substrate heterogeneity is a main determinant of spatial gene expression in colonies of Aspergillus niger. This question was addressed by analyzing whole-genome gene expression in five concentric zones of 5-day-old sugar beet pulp grown colonies. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

10 Samples

Download data: CEL

(Submitter supplied) We have studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA-sequencing we showed that, 24 hours after exposure to straw, gene expression of known plant cell wall degrading enzymes represents a huge investment for the cells (about 20 % of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal degradative arsenal. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14910

9 Samples

Download data: TXT

(Submitter supplied) Galactose catabolism in Aspergillus nidulans is regulated by at least two regulators, GalR and GalX. In Aspergillus niger only GalX is present, and its role in D-galactose catabolism in this fungus was investigated. Phenotypic and gene expression analysis of a wild type and a galX disruptant revealed that GalX does not substitute for the absence of GalR in A. niger, it regulates the D-galactose oxido-reductive pathway, but not the Leloir pathway. more...

Organism:

Aspergillus niger CBS 513.88; Aspergillus niger

Type:

Expression profiling by array

Platform:

GPL6758

4 Samples

Download data: CEL

(Submitter supplied) The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

59 Samples

Download data: CEL

(Submitter supplied) Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16343

8 Samples

Download data: TXT

(Submitter supplied) This experiment was designed to test the change in gene expression in the absence of the transcription factor, CreA. Two media conditions were tested to determine the role of this transcription factor in repressing (glucose) and derepressing (ethanol) carbon sources.

Organism:

Aspergillus fumigatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23268

8 Samples

Download data: TXT

(Submitter supplied) Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening starvation conditions, carbon from extra- and intracellular resources becomes mobilized to fuel fungal self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal starvation responses in a temporal and spatial resolution. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

6 Samples

Download data: CEL

(Submitter supplied) The aim of this study was to better understand the contribution of the transcriptional activators GaaR, RhaR and AraR in regulation of pectin degradation in A. niger.

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21721

32 Samples

Download data: TXT

(Submitter supplied) This work presents an exploration of submerged differentiation of the ubiquitous saprophyte and industrially important fungus, Aspergillus niger, in response to a limited availability of a sole carbon and energy source, maltose. In aspergilli and other mold fungi, asexual reproduction through formation of elaborate conidiogenic structures normally requires an aerial interface. This requirement is bypassed in submerged culture in response to severe nutrient limitation. more...

Organism:

Aspergillus niger CBS 513.88; Aspergillus niger

Type:

Expression profiling by array

Platform:

GPL6758

9 Samples

Download data: CEL

(Submitter supplied) The filamentous ascomycete Aspergillus niger has received increasing interest as a cell factory, being able to efficiently degrade plant cell wall polysaccharides as well as having an extensive metabolism to convert the released monosaccharides into value added compounds. The pentoses D-xylose and L-arabinose are the most abundant monosaccharides in plant biomass after D-glucose, being major constituents of xylan, pectin and xyloglucan. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21818

90 Samples

Download data: TXT

(Submitter supplied) Saprotrophic fungi, such as Aspergillus niger, grow as mycelial colonies that are often considered uniform entities. To test this uniformity, we analyzed pie-slice sections of a colony grown on spatially separated substrates (glucose, wheat bran, sugar beet pulp) using transcriptomics, proteomics and metabolomics. The colony tuned its response to the local carbon source composition. Plant biomass degrading CAZymes and intracellular carbon catabolic enzymes were more abundant in parts of the colony containing the corresponding sugars. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25482

27 Samples

Download data: TXT

(Submitter supplied) Mycelia of filamentous fungi explore new substrates by means of hyphae that extend from the periphery of the colony. Previously, it has been shown by immuno-labelling, reporter studies and in situ hybridization that these exploring hyphae are heterogenic with respect to protein secretion and transcription. We performed single hyphal tip RNA profiling using microarrays to assess the differences in RNA accumulation in neighboring exploring hyphae

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

5 Samples

Download data: CEL

(Submitter supplied) Purpose: Expression profiling of two ORFs encoding putative transcription factors: An07g07370 (TF1/MjkA) and An12g07690 (TF2/MjkB), and a histone deacetylase (An09g06520, HdaX) under carbon-limited batch cultivations (biological duplicate runs) in Aspergillus niger. Methods: Single deletion strains for TF1, TF2 and HD, respectively, (ii) a double deletion strain for TF1 and TF2, and (iii) individual conditional overexpression mutants for TF1, TF2 and HD using the Tet-on system were analysed. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25519

28 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Dichomitus squalens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24128

20 Samples

Download data: TXT

(Submitter supplied) Expression of genes encoding plant biomass degrading enzymes in ascomycetes is controlled by transcriptional activators that respond to the presence of monomeric components of plant polymers. It can be expected that a similar system exists in basidiomycetes, but no homologs of the ascomycete regulators could be identified in basidiomycetes.

Organism:

Dichomitus squalens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24128

6 Samples

Download data: GFF3, TXT

(Submitter supplied) Expression of genes encoding plant biomass degrading enzymes in ascomycetes is controlled by transcriptional activators that respond to the presence of monomeric components of plant polymers. It can be expected that a similar system exists in basidiomycetes, but no homologs of the ascomycete regulators could be identified in basidiomycetes.

Organism:

Dichomitus squalens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24128

14 Samples

Download data: TXT

(Submitter supplied) Knowledge of the biological and technical variation for fermentor-grown Aspergillus niger cultures is needed to design DNA microarray experiments properly. We cultured A. niger in batch-operated fermentor vessels and induced with D-xylose. Transcript profiles were followed in detail by qPCR for 8 genes. A variance components analysis was performed on these data to determine the origin and magnitude of variation within each process step for this experiment. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

7 Samples

Download data: CEL