Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome study on Aspergillus niger during citrate fermentation.

ABSTRACT: We report the genes regulated during citrate fermentation. Examination of 5 different time points during fermentation in Aspergillus niger H915-1.

ORGANISM(S): Aspergillus niger

SUBMITTER: Xian Yin

PROVIDER: E-GEOD-74544 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome study on Aspergillus niger during citrate fermentation.

Project description:We report the genes regulated during citrate fermentation.

2016-06-30 | GSE74544 | GEO

Comparative proteomic analysis of Bacillus subtilis and Aspergillus niger in Black Soldier Fly co-fermentation

Project description:the original data of black soldier fly larva mass fermentation with Bacillus subtilis and Aspergillus niger, analyzed by Chinese biotechnology company, published by Chinese Academy of Tropical Agricultural Sciences Environment and Plant Protection Institute for research only.

2023-10-25 | PXD037713 | JPOST Repository

Differential expression analysis of Aspergillus niger genes in mRMA level between in seed medium and fermentation media for L-malic acid production

Project description:Generally, A. niger undergoes two steps consisting of seed stage and fermentation stage to synthesize malic acid. However, it remains unknown which metabolic pathways, regulators, and key genes respond to the transition from seed medium to fermentation medium. In this study, we obtained the total mRMA of a high L-malate-yielding strain A. niger RG0095 at seed stage and fermentation stage, respectively, and performed a global differential expression analysis.

2024-03-15 | GSE235528 | GEO

Aspergillus niger mutants: induction by various carbon sources

Project description:This SuperSeries is composed of the following subset Series: GSE37758: Aspergillus niger : Control (fructose) vs. steam-exploded sugarcane induction (SEB) GSE37760: Aspergillus niger : Control (fructose) vs. xylose + arabinose (XA) Refer to individual Series

2012-05-06 | E-GEOD-37795 | biostudies-arrayexpress

Attachment of Bacillus subtilis to the hyphae of Aspergillus niger results in altered metabolism and defense mechanisms in both partner

Project description:Interaction of microbes affects the growth, metabolism and differentiation of members of the community. While direct and indirect competitions, like spite and nutrient consumption have negative effect on each other, microbes also evolved in nature not only to fight, but in some cases to adapt or support each other while increasing the fitness of the community. Presence of bacteria and fungi in the soil results in interactions and various examples were described, including mutualism. Bacilli attach to the plant root and form complex communities in the rhizosphere. Bacillus subtilis, when grown in the presence of Aspergillus niger interacts with the fungal partner, attaches and grows on the hyphae. Using dual transcriptome experiment, we show that both fungi and bacteria alter their metabolisms during the interaction. Interestingly, the transcription of genes related to the antifungal and antibacterial defense mechanism of B. subtilis and A. niger, respectively, are decreased upon attachment of bacteria to the mycelia. Our microarray experiments provide a novel insight into the mutual interaction of a bacterium and a fungus. Aspergillus niger were grown with and without Bacillus subtilis. Biological triplicates were made for both conditions, Affymetrix microarray experiments were performed on these samples.

2014-10-07 | E-GEOD-46187 | biostudies-arrayexpress

Determination of variability of fermentor-grown Aspergillus niger

Project description: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. 6 Fermentor cultures were selected to determine technical and biological variation for all 14554 ORFs present on this array type. Keywords: Validation of microarrays; variation analysis; experimental design For 5 weeks, 4 batch-fermentation per week were run in which A. niger was grown on 100 mM sorbitol. At 14 hours after oxygen supply had switched from headspace to sparger-inlet each fermentor was induced with either 0.1 mM D-xylose or 0.1 mM sorbitol. Samples were harvested just before induction and 1 hour after induction. Per week, 3 fermentors were induced with D-xylose and 1 fermentor was induced with sorbitol. Six samples were selected to be put on microarrays based on their biomass density, time distribution, magnitude of xylose-induced genes as measured by qPCR, fermentor vessel number.

2008-12-30 | E-GEOD-11405 | biostudies-arrayexpress

Correlating citric acid formation and manganese limitation in Aspergillus niger using transcriptome and proteome analysis

Project description:Aspergillus niger is well known for its capability to produce citrate in high amounts but the detailed metabolic response causing citrate production has not been fully elucidated. Manganese is known to have an important effect as its limitation is a requirement to obtain high-level citrate formation. To identify the translational regulation causing citric acid overflow metabolism, transcriptome and proteome data from cultivations in manganese limitation and manganese excess conditions were analyzed. In addition to four already described main responses, two novel events were identified. The first metabolic response was down regulation of phosphoenolpyruvate carboxykinase (PEPCK) during manganese limited conditions, which was confirmed by in vivo experiments. Down regulation of the first step in the gluconeogenesis, while maintaining a high activity through glycolysis, promoted secretion of citrate into the medium as an alternative regulatory mechanism for adjusting the intracellular concentrations of TCA intermediates. The other novel observation was down regulation of two cation transporters at manganese limited conditions. It was hypothesized that lowered cation transport across the mitochondrial membrane reduced the ability of the cell to maintain homeostasis thereby favoring citric acid secretion. Finally, upregulation of an ABC transporter was measured, which was assumed to be a citrate permease.

2014-10-03 | GSE61985 | GEO

Regulation of inulin and sucrose utilization by Aspergillus niger AmyR and InuR

Project description:The aim of this study was to investigate the regulatory role of Aspergillus niger AmyR and InuR during growth on inulin and sucrose

2023-05-03 | GSE204768 | GEO

A tri-species Aspergillus array (niger arrays)

Project description:The full genome sequencing of the ﬁlamentous fungi Aspergillus nidulans, Aspergillus niger and Aspergillus oryzae has opened the possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are presenting an Aﬀymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose-and xylose media has been performed, and used to validate the performance of the micro array. By doing gene comparisons of all three species, and cross-analysing this with the expression data, 23 genes, including the xylose transcriptional activator XlnR, have been identiﬁed to be a conserved response across the Aspergillus sp. Promoter analysis of the upregulated genes in all three species suggest the XlnR-binding site to be 5’-GGNTAAA-3’. We are thus presenting a validated tool for transcription analysis of three Aspergillus species and a methodology for comparative transcriptomics. Keywords: Physiological response

2008-02-15 | GSE9276 | GEO

Determination of variability of fermentor-grown Aspergillus niger

2008-12-31 | GSE11405 | GEO