Aspergillus niger
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PROVIDER: PRJNA119011 | ENA |
REPOSITORIES: ENA
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Project description: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.
2010-04-08 | GSE17329 | GEO
Project description: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.
2010-04-08 | E-GEOD-17329 | biostudies-arrayexpress
Project description:Transcriptional profiling of the A. niger WT (N402) strain treated with xylan (1%, w/v) for 6, 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases after treatment with the polysaccharide xylan. The experiment was further validated by enzymatic assays. Three-condition experiment: WT-Xylan for 6, 12 and 24 h at 30oC in batch culture. Firstly, the WT (N402) strain was grown in minimal medium with fructose as carbon source (control), and then transferred to 1% (w/v) xylan as carbon source. 2 biological replicates per time point.
2010-10-21 | E-GEOD-24848 | biostudies-arrayexpress
Project description:Transcriptional profiling of A. niger comparing different strains (WT, M-NM-^TXlnR, M-NM-^TaraR and M-NM-^TaraRM-NM-^TXlnR) treated with 25mM xylose + 25mM arabinose for 2 and 8h. The main objective was to identifiy genes related to primary metabolism and carbohydrate metabolism in general, for instance, cellulases and hemicellulases. The study will compare the differences between WT strain and the strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant,after treatment with xylose+arabinose (XA treatment). The experiment was further validated by real-time PCR and enzymatic assays. Two-condition experiment : A. niger mutant strains on XA for 2 and 8 h at 30 oC in batch culture. Firstly, the strains were pre-grown in minimal medium with fructose as carbon source (control), and then transferred to xylose+arabinose (25 mM each) as carbon source.
2012-05-06 | E-GEOD-37760 | biostudies-arrayexpress
Project description:Transcriptional profiling of A. niger comparing mutant strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant (M-NM-^TXlnR, M-NM-^TaraR and M-NM-^TaraRM-NM-^TXlnR, repsectively) treated with steam-exploded sugarcane bagasse (SEB) for 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases in mutant strains grown on SEB, with indirect comparisons with the WT strain grown on SEB [the (WT/SEB) data deposited in GSE24798]. The experiment was further validated by real-time PCR and enzymatic assay. Two-condition experiment : A. niger mutant strains on SEB for 12 and 24 h at 30 oC in batch culture. Firstly, the strains were pre-grown in minimal medium with fructose as carbon source (control), and then transferred to SEB as carbon source.
2012-05-06 | E-GEOD-37758 | biostudies-arrayexpress
Project description:This approach aims at searching unidentified regulatory roles of the AreB transcription factor in the overall carbon metabolism of A. niger. A full areB gene deletion mutant was constructed and characterized in A. niger ATCC 1015. Both strains were grown on glucose or glycerol using ammonia as nitrogen source in batch cultivations and the transcriptome was analyzed using three biological replicated transcriptome experiments. Two areB gene deletion replicates, one on glucose and one on glycerol were discarded due to bad quality and therefore not included in the analysis. Samples for RNA extraction were collected and further processed for hybridization in custom designed Affymetrix microarrays containing probes for three Aspergillus species including A. niger.
2011-01-31 | GSE21015 | GEO
Project description:Transcriptional profiling of A. niger comparing WT strain vs. ÎXlnR strain treated with steam-exploded sugarcane bagasse (SESB) for 6, 12 and 24 h. The main objective was to identifiy genes related to cellulases and hemicellulases, comparing the differences between WT strain and the strain with the disrupted xylanolytic transcriptional activator gene, XlnR, after treatment with steam-exploded sugarcane. The experiment was further validated by real-time PCR, mass spectrometry of secreted proteins and enzymatic assays. Three-condition experiment : WT-SESB or ÎXlnR-SESB for 6, 12 and 24 h at 30 oC in batch culture. Firstly, WT and ÎXlnR strains were grown in minimal medium with fructose as carbon source (control), and then transferred to SESB as carbon source.
2010-10-20 | E-GEOD-24798 | biostudies-arrayexpress
Project description:Expression data from batch cultivations of Aspergillus niger wild type strain ATCC 1015 and adrA, facB and creA deletion mutants constructed on ATCC 1015 background strain with glucose or glycerol as carbon sources. Genome-wide transcriptome analysis was used to identify genes either affected directly or indirectly by each transcription factor investigated during growth on a repressing or a derepressing carbon source. For this purpose, batch cultivations under well-controlled conditions were performed with Aspergillus niger wild type strain ATCC 1015 and the three deletion mutants of the corresponding transcription factors AdrA, FacB and CreA. Samples for RNA extraction were collected and further processed for hybridization in custom-designed Affymetrix microarrays containing probes for three Aspergillus species, including A. niger. Triplicate batch fermentations of each of the four Aspergillus niger strains used, the wild type A. niger strain ATCC 1015 and three gene deletion mutants, were carried out using glucose or glycerol as carbon source, and transcriptome analysis was performed. Biomass from each batch cultivation was harvested in the exponential phase of growth and further processed for RNA extraction and hybridization on Affymetrix microarrays.
2011-01-31 | E-GEOD-19952 | biostudies-arrayexpress
Project description:Expression data from batch cultivations of Aspergillus niger wild type strain ATCC 1015 and adrA, facB and creA deletion mutants constructed on ATCC 1015 background strain with glucose or glycerol as carbon sources. Genome-wide transcriptome analysis was used to identify genes either affected directly or indirectly by each transcription factor investigated during growth on a repressing or a derepressing carbon source. For this purpose, batch cultivations under well-controlled conditions were performed with Aspergillus niger wild type strain ATCC 1015 and the three deletion mutants of the corresponding transcription factors AdrA, FacB and CreA. Samples for RNA extraction were collected and further processed for hybridization in custom-designed Affymetrix microarrays containing probes for three Aspergillus species, including A. niger.
2011-01-31 | GSE19952 | GEO
Project description:Aspergillus niger produces a variety of lignocellulolytic enzymes (cellulases, hemicellulases, among others) and is regarded as cell factory for the production of heterologous proteins. Therefore, there is a growing interest in the study of its genes and the understanding of the cellular mechanisms in order to expand its applications. On the other hand, we have shown that enzyme production by A. niger is higher when grown forming biofilms than when grown conventionally in submerged systems. The objective of this study was to perform a global transcriptomic analysis and an expression analysis of both lignocellulases and biofilm regulatory genes as compared to A. niger in submerged culture. DNA microarray assays were performed to investigate the global gene expression which yielded information on the expression of more than 90% of A. niger genes. To further this comparison, the two culture systems were supplemented with different carbon sources (glucose, lactose, xylose and maltose) to establish a differential gene expression under different culture conditions. Also, to validate the differential expression qPCR was performed for quantitative comparison of the transcriptional level of genes in both culture systems.
2016-08-23 | GSE85945 | GEO