|
| Status |
Public on Sep 20, 2012 |
| Title |
Wild type A.niger, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
wild type_D-galactose_2h
|
| Organism |
Aspergillus niger |
| Characteristics |
strain background: N402
genotype/variation: cspA, wild type
tissue: mycelium
incubated in: minimal medium with 25 mM D-galactose for 2hr
|
| Treatment protocol |
Pre-cultures for DNA and RNA isolation were grown overnight in 1L Erlenmeyer flasks containing 250 ml CM with 2% D-fructose. For microarray analysis, the pre-grown cultures were washed with MM and transferred to 250 ml Erlenmeyer flasks containing 50 ml MM + 25 mM monosaccharide or 1% polysaccharide and were incubated for an additional 2 hours. After incubation, the mycelium was harvested by vacuum filtration, dried between towels and immediately frozen in liquid nitrogen.
|
| Growth protocol |
The A. niger strains used in this study are N402 (reference, genotype: cspA) and FP-315.1 (galX disruptant, genotype: cspA, 5 ΔkusA::amdS+, galX::pyrG+). Spore plates contained Complete Medium + 2% glucose. All liquid cultures were grown in Erlenmeyer flasks on a rotary shaker (250 rpm) at 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) 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 ug 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.
|
| Description |
Gal 2
|
| Data processing |
Affymetrix CEL-data files were preprocessed by using the statistical language and environment R (R Development Core Team, 2007) version 2.6.1. The probe intensities were normalized for background by using the robust multiarray average method (Irizarry, 2003) by using only perfect match (PM) probes. Normalization was performed subsequently by using the quantiles algorithm (Bolstad, 2003). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).
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| |
|
| Submission date |
Aug 20, 2012 |
| Last update date |
Sep 20, 2012 |
| Contact name |
miaomiao Zhou |
| E-mail(s) |
miaomiaozhou88@hotmail.com
|
| Phone |
+ 31 (0)30 2122600
|
| Organization name |
centre of fungal biodiversity, Utrecht, KNAW
|
| Department |
fungal physiology
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6758 |
| Series (1) |
| GSE40219 |
The galactose regulator GalX regulates the D-galactose oxido-reductive pathway in Aspergillus niger. |
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