|
| Status |
Public on Apr 23, 2018 |
| Title |
Mix_sugar_time_4 replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
A. niger wild type grown on mix sugars 33 hours
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: Wild type N402
|
| Treatment protocol |
Mixture of 10 mM monomeric sugars (D-glucose, D-fructose, D-mannose, D-galactose, L-rhamnose, D-xylose, L-arabinose, D-galacturonic acid) and maltose (Sigma-Aldrich) was added into 50 mL MM in 250 mL Erlenmeyer flasks. The cultures were inoculated with mycelial aliquots from the pre-cultures (1 g wet-weight per flask) and incubated at 250 rpm, at 30°C. Samples from 12, 18, 24 and 33 h were used for microarrays.
|
| Growth protocol |
A. niger N402 wild type was pre-cultured in 1 L Erlenmeyer flasks in 200 mL complete medium (CM), pH 6.0, that contained Aspergillus minimal medium (MM) (de Vries R, et al., 2004. Appl Env Mic). The pre-cultures were inoculated with 106 spores/mL and incubated at 250 rpm for 16 h at 30°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol reagent (Invitrogen) and purified using TRIzol® Plus RNA Purification Kit (Sigma-Aldrich) according to the instructions of the manufacturer.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled antisense cRNA was produced from 2 µg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 µg of cRNA was hybridized to Affymetrix A. niger Genome Gene chips (GPL6758). GeneChips were washed and stained in an automated process.
|
| Scan protocol |
GeneChips were scanned.
|
| Data processing |
Microarray data was analyzed using Affymetrix Expression Console software v1.4.1.46 with the normalized values in linear scale. The probe intensities were normalized for background by the robust multiarray average (RMA) method which makes use of only the perfect match probes. Gene expression values were calculated with the medianpolish summary method from the PM probes.
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| |
|
| Submission date |
May 02, 2017 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Ronald de Vries |
| E-mail(s) |
fungalphysiology@gmail.com
|
| Phone |
+ 31 (0)30 2122600
|
| Organization name |
Centre of fungal biodiversity
|
| Department |
fungal physiology
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6758 |
| Series (1) |
| GSE98434 |
The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA |
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