|
| Status |
Public on Dec 31, 2008 |
| Title |
D-xylose sample 86 replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
induced 0.1 mM xylose
|
| Organism |
Aspergillus niger |
| Characteristics |
Strain 872.11
|
| Treatment protocol |
14 hours after the aeration switch to sparger, 50 mL sample was removed from the fermentor. Either D-xylose or sorbitol dissolved in MM (final concentration in fermentor 0.1 mM) was added. One hour after induction, a second 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.
|
| Description |
none
|
| Data processing |
RMA values were determined by Agilent's GeneSpring GX software (version 7.3.1) using the RMA preprocessor.
|
| |
|
| Submission date |
May 09, 2008 |
| Last update date |
May 29, 2008 |
| 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) |
| GSE11405 |
Determination of variability of fermentor-grown Aspergillus niger |
|
