|
| Status |
Public on Sep 01, 2009 |
| Title |
DGDG_T=1 |
| Sample type |
RNA |
| |
|
| Source name |
induced 1 mM DGDG, T=1 hour
|
| Organism |
Aspergillus niger |
| Characteristics |
Strain 872.11
|
| Treatment protocol |
14 hours after the aeration switch to sparger, 20 mL sample was removed from the fermentor. Either complex wheat gluten oil, or olive oil, or pure DGDG (digalactosyldiglycerides) dissolved in MM with 0.2% Triton X-100 as emulsifier (final concentration in fermentor 1 mM oil, 0.002% Triton X-100) was added to a fermentor. To one fermentor, only MM with 0.2% Triton X-100 (final concentration in fermentor: 0.002%) was added as negative control fermentation. At 30 minutes, 1 hour or 2 hours after induction, a 20 mL-sample was removed from the fermentor and the mycelium was snap-frozen in liquid N2 until further use.
|
| Growth protocol |
Fermentor vessels containing 2.2 liters of minimal medium, supplements, and 100 mM sorbitol were inoculated with 1.1e6 spores per mL and maintained at 30 C. Aeration was done over headspace (50 L/h) while stirring at 300 rpm until dissolved oxygen concentration dropped below 60%. Then, stirrer speed was adjusted to 750 rpm and aeration switched to sparger inlet. The culture was allowed to grow for 14 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen mycelium was ground using a dismembrator, followed by a trizol-chloroform extraction using the Qiagen Rneasy mini columns according to the “yeast protocol”.
|
| Label |
biotin
|
| Label protocol |
Extracted totalRNA was processed following the Affymetrix user manual (Eukaryotic Target) using the One-cycle target labeling and control reagents kit (Affymetrix). 15 ug of cRNA was used for labeling.
|
| |
|
| Hybridization protocol |
Washing, staining, and hybridization was done according to the Hybridization, Wash, and Stain kit (Affymetrix) according to the manufacturers' recommendations
|
| Scan protocol |
Arrays were scanned on an Agilent G2500A Gene Array scanner. Pixel value was 3 um, wavelength 570 nm. Arrays were scanned on two days (see Sample description).
|
| Description |
T=1_DGDG.CEL
scanned on day 1
|
| Data processing |
RMA values were calculated using GeneSpring 7.3.1 (Agilent Technologies), where the RMA preprocessor was used to import the .CEL files.
|
| |
|
| Submission date |
Jan 05, 2009 |
| Last update date |
Jan 05, 2009 |
| Contact name |
Leo H De Graaff |
| E-mail(s) |
leo.degraaff@wur.nl
|
| Phone |
+31 317 484691
|
| Fax |
+31 317 483829
|
| URL |
http://www.mib.wur.nl
|
| Organization name |
Wageningen University and Research Centre
|
| Department |
Microbiology
|
| Lab |
Fungal Genomics
|
| Street address |
Dreijenplein 10
|
| City |
Wageningen |
| ZIP/Postal code |
6703 HB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6758 |
| Series (1) |
| GSE14285 |
The transcriptional response of bioreactor-grown Aspergillus niger cultures towards three oils |
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