GEO DataSets

(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

(Submitter supplied) 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. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

20 Samples

Download data: CEL

(Submitter supplied) The industrially important fungus Aspergillus niger feeds naturally on decomposing plant material, for which it is equipped with a range of enzyme systems. A significant proportion of plant material are lipids that might be available either as for energy storage or as membrane building blocks. With 63 potential lipase-encoding genes in its genome, A. niger has the tools to degrade these extracellular lipids. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

16 Samples

Download data: CEL

(Submitter supplied) d-serine is naturally present throughout the human body. It is also used as add-on therapy for treatment-refractory schizophrenia. d-Serine interacts with the strychnine-insensitive glycine binding site of NMDA receptor, and this interaction could lead to potentially toxic activity (i.e., excitotoxicity) in brain tissue. The transcriptomic changes that occur in the brain after d-serine exposure have not been fully explored. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS3643

Platform:

GPL1355

24 Samples

Download data: CEL

Analysis of forebrains of animals treated with up to 500 mg/kg D-serine for 96 hours. D-serine is involved in many physiological processes through its interaction with the glycine binding site of the NMDA receptor. Results provide insight into the impact of D-serine exposure on neuronal functions.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 agent, 6 dose sets

Platform:

GPL1355

Series:

GSE10748

24 Samples

Download data: CEL

(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; Aspergillus niger CBS 513.88

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) The genes of the non-phosphorylative L-rhamnose catabolic pathway have been identified for several yeast species. In Pichia stipitis, all L-rhamnose pathway genes are organized in a cluster, which is conserved in Aspergillus niger, except for the lra-4 ortholog (lraD). The A. niger cluster also contains the gene encoding the L-rhamnose responsive transcription factor (RhaR) that has been shown to control the expression of genes involved in L-rhamnose release and catabolism. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21721

10 Samples

Download data: TXT

(Submitter supplied) Colonies of Aspergillus niger secrete proteins throughout the colony except for the sporulating zone. Inactivation of flbA results in colonies that are unable to reproduce asexually and that secrete proteins throughout the mycelium. In addition, the ΔflbA strain shows cell lysis and has thinner cell walls. This pleiotropic phenotype is associated with differential expression of 38 transcription factor genes. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21090

4 Samples

Download data: DIFF

(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) 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 genome of the filamentous fungus Aspergillus niger is rich in genes encoding pectinases, a broad class of enzymes that have been extensively studied due to their use in industrial applications. The sequencing of the A. niger genome provided more knowledge concerning the individual pectinolytic genes, but relatively little is still known about the regulatory genes involved in pectin degradation. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

4 Samples

Download data: CEL

(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) Background: HacA/Xbp1 is a conserved bZIP transcription factor in eukaryotic cells which regulates gene expression in response to various forms of secretion stress and as part of secretory cell differentiation. In the present study, we replaced the endogenous hacA gene of an Aspergillus niger strain with a gene encoding a constitutively active form of the HacA transcription factor (HacACA). The impact of constitutive HacA activity during exponential growth was explored in bioreactor controlled cultures using transcriptomic analysis to identify affected genes and processes. more...

Organism:

Aspergillus niger CBS 513.88; Aspergillus niger

Type:

Expression profiling by array

Platform:

GPL6758

12 Samples

Download data: CEL

(Submitter supplied) The Tup1-Cyc8 (Ssn6) complex is a well characterized and conserved general transcriptional repressor complex in eukaryotic cells. Here, we report the identification of the Tup1 (TupA) homolog in the filamentous fungus Aspergillus niger in a genetic screen for mutants with a constitutive expression of the agsA gene. The agsA gene encodes a putative alpha-glucan synthase, which is induced in response to cell wall stress in A niger. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

4 Samples

Download data: CEL

(Submitter supplied) The goal of this study was to conduct an in-depth analysis of the human placental transcriptome. RNA was extracted from 16 placental samples using TRIzol following the manufacturer’s protocol. All samples were spiked with 96 External RNA Controls Consortium (ERCC) ExFold RNA transcripts. Ribosomal RNAs were depleted from samples using Ribo-Zero Gold and sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation kits. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

16 Samples

Download data: CSV

(Submitter supplied) We identified the D-galacturonic acid (GA) responsive transcriptional activator GaaR of the saprotrophic fungus Aspergillus niger, which was found to be essential for growth on GA and polygalacturonic acid (PGA). Growth of the ΔgaaR strain was reduced on complex pectins. Genome-wide expression analysis showed that GaaR is required for the expression of genes necessary to release GA from PGA and more complex pectins, to transport GA into the cell and to induce the GA-catabolic pathway. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21721

16 Samples

Download data: TXT

(Submitter supplied) We report the genes regulated during citrate fermentation.

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21090

6 Samples

Download data: FASTA, TXT

(Submitter supplied) Aspergillus niger fulfills an important role in nature in nutrient cycling and is a main cell factory for the industrial production of metabolites and enzymes. Inactivation of flbA in A. niger results in thinner cell walls, increased cell lysis, abolished sporulation, and an increased secretome complexity. A total of 36 transcription factor genes are differentially expressed in ∆flbA. Here, seven of these genes (abaA, aslA, aslB, azf1, htfA, nosA, and srbA) were inactivated. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34135

9 Samples

Download data: TSV, XLSX

(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