|
| Status |
Public on Aug 04, 2021 |
| Title |
submerged growth on sugar beet pulp for 24 hours biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Mycelium
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: N402
treatment: during SBP degradation after 24 hour incubation
|
| Treatment protocol |
One gram (wet weight) of the mycelium was transferred to 250 mL Erlenmeyer flasks containing 50 mL MM supplemented with 1% SBP or PGA (Sigma-Aldrich) and incubated for 8 h and 24 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 |
Jun 01, 2021 |
| Last update date |
Aug 04, 2021 |
| Contact name |
Ronald de vries |
| E-mail(s) |
fungalphysiology@gmail.com
|
| Phone |
+31(0)30-2122600
|
| Organization name |
westerdijkinstitute
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6758 |
| Series (1) |
| GSE175954 |
Comparative study of gene expression in Aspergillus niger solid and submerged growth during sugar beet pulp utilization |
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