Aspergillus niger
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA134633 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: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 Single tips from 5 neighboring exploring hyphae from a single colony were selected for RNA extraction, amplification and hybridization on Affymetrix microarrays
2011-05-17 | E-GEOD-25497 | biostudies-arrayexpress
Project description: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
2011-05-17 | GSE25497 | GEO
Project description:Using transcriptomics, the strain-specific metabolism was mapped for two whole-genome sequenced strains of Aspergillus niger Keywords: Strain comparison
2011-03-07 | GSE10983 | GEO
Project description:Transcriptome comparison of Bacillus subtilis NCIB3610 attached to the hyphae of Aspergillus niger CB 119.1 compared to Bacillus subtilis NCIB3610 cells in the supernatant of the same culture. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can also be found in the submitted paper.
2014-09-09 | GSE46682 | GEO
Project description:Using transcriptomics, the strain-specific metabolism was mapped for two whole-genome sequenced strains of Aspergillus niger Keywords: Strain comparison Two strains grown in controlled bioreactors, three biological replicates each.
2011-03-07 | E-GEOD-10983 | biostudies-arrayexpress
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
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
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 Two conditions (glucose and xylose) and three biological replicates
2008-02-15 | E-GEOD-9276 | biostudies-arrayexpress
Project description:Colonies of Aspergillus niger secrete proteins throughout the colony except for the sporulating zone. Strains in which the sporulation gene flbA is deleted do not reproduce asexually and secrete proteins throughout the mycelium. Moreover, ΔflbA hyphae lyse and have thinner cell walls. This pleiotropic phenotype is associated with differential expression of 36 transcription factor genes, of which msnB was inactivated in this study. Whole genome expression analysis of wild-type and ΔmsnB colonies showed differential expression of genes encoding secreted proteins, genes involved in the oxidoreductive balance, and in (secondary) metabolism. Biomass formation, sporulation, and the secretome in the medium were not affected in strain ΔmsnB. In contrast, ΔmsnB secreted more protein when compared to wild type. Taken together, msnB affects protein secretion and is a potential lead for improving A. niger as a cell factory.
2018-10-01 | GSE104669 | GEO
Project description:Transcriptome comparison of Bacillus subtilis NCIB3610 attached to the hyphae of Aspergillus niger CB 119.1 compared to Bacillus subtilis NCIB3610 cells in the supernatant of the same culture. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can also be found in the submitted paper. B subtilis NCIB3610 cells were grown in the presence of Aspergillus niger CB 119.1 hyphae for 3 hours. The mycelium and the attached bacteria were separated from the non-attached B. subtilis cells via filtration through Miracloth. The mycelia and attached bacteria were briefly rinsed with TY medium, dried, and the sample was frozen in liquid nitrogen. Bacterial cells in the flow-through medium fraction were harvested by centrifugation at 10.397 g for 1 min. To extract RNA mainly from the bacterial cells, lysozyme solution and RiboLock (Thermo Scientific) was added followed by incubation at 37 C for 30 minutes. Further RNA extraction was performed with the Macaloid/Roche method as described before (van Hijum et al., 2005, Kovács and Kuipers, 2011) but omitting the bead beater treatment and using RiboLock.
2014-09-09 | E-GEOD-46682 | biostudies-arrayexpress