|
| Status |
Public on Aug 11, 2020 |
| Title |
Aspergillus niger wild type grown on guar-gum 2 hours, replicate 2 (re-analyzed) |
| Sample type |
RNA |
| |
|
| Source name |
A. niger wild type growing on guar-gum
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: N402
genotype: cspA1 (wild type)
tissue: mycelium
age: 2 hours
substrate: 1% guar-gum
|
| Treatment protocol |
One gram (wet weight) of the mycelium was transferred to 250 mL Erlenmeyer flasks containing 50 mL MM supplemented with 1% guar gum (Sigma-Aldrich) and incubated for 8 h, 24 h and 48 h.
|
| Growth protocol |
Aspergillus niger N402 was propagated and grown on complete medium (CM) or minimal medium (MM). Liquid cultures were grown in a rotary shaker at 250 rpm and 30C. Transfer experiment was performed by growing the strain for 16 h in 1 L Erlenmeyer flasks that contained 250 mL CM supplemented with 2% D-fructose as carbon source. The mycelium was harvested by filtration and washed with MM without a carbon source.
|
| 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 GeneChips (GPL6758). GeneChips were washed and stained in an automated process.
|
| Scan protocol |
GeneChips were scanned.
|
| Data processing |
Microarray data was analyzed using the Bioconductor tool package version 2.8 (http://www.bioconductor.org/) together with house-made Perl (version .5.0) and Python (version 3.0) scripts. Probe intensities were normalized for background by the robust multi-array average (RMA) method using the R statistical language and environment. This method makes use of only perfect match (PM) probes. Normalization was processed by the quantiles algorithm. The median polish summary method was used to calculate the gene expression values.
|
| |
|
| Submission date |
Aug 31, 2018 |
| Last update date |
Aug 11, 2020 |
| 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) |
| GSE119310 |
The molecular response of Aspergillus niger to guar gum |
|
| Relations |
| Reanalysis of |
GSM2600961 |
