|
| Status |
Public on Jan 26, 2011 |
| Title |
PH1_untreated_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
PH1_complete medium_non-treated control
|
| Organism |
Fusarium graminearum |
| Characteristics |
strain: PH1 (syn. NRRL31084)
|
| Growth protocol |
106 conidia were inoculated into 300 ml flasks each containing 100 ml complete medium (Leslie & Summerell, The Fusarium Laboratory Manual, Blackwell Publishing) and cultivated at 23°C with shaking at 150 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from mycelia grown in vitro with the Qiagen RNeasy Plant Mini Kit following the manufacturer’s protocol. The optional on-column DNase digestion step was performed using RNase-free DNase (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
For sample preparation and array processing the Agilent protocol “One-color microarray-based gene expression analysis (Quick Amp Labelling)” was used (http://www.chem.agilent.com).Briefly, the recommended volume of control RNAs (Agilent One-Color RNA Spike-In Kit) was added to 200 ng of total RNA. Thereafter, cyanine 3´- labelled cRNA was produced, using the Agilent Quick Amp Kit (one-color) according to the manufacturer’s protocol. Labelled cRNA was purified with the RNeasy mini kit (Qiagen). Yield and Cy3 incorporation rates were analyzed using a NanoDrop ND-1000 UV-VIS spectrophotometer. In addition, size distribution of cRNAs was assessed by a BioAnalyzer 2100.
|
| |
|
| Hybridization protocol |
For hybridizations, 600 ng of Cy3-labelled cRNA was used. Hybridization was set up in an Agilent Microarray Hybridization Chamber (G2534A) and incubated in an Agilent Hybridization Oven (G2545A) at 65°C and 10 rpm for 17 h. Thereafter, suggested washing steps were performed.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x15K array slides (scan resolution: 5 µm resolution).
|
| Description |
Gene expression in untreated control culture
|
| Data processing |
The microarray scan data were analyzed by Agilent's Feature Extraction software_v10.5 obtaining background subtracted and spatially detrended signal intensities. These 'gProcessedSignal' data were converted to gene signals by a median polish algorithm as implemented in the RMA algorithm. Gene signals were normalized between experiments by quantile normalization.
|
| |
|
| Submission date |
Nov 03, 2010 |
| Last update date |
Jan 26, 2011 |
| Contact name |
Rayko Becher |
| E-mail(s) |
rayko.becher@landw.uni-halle.de
|
| Organization name |
Martin-Luther-University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences
|
| Department |
Department of Phytopathology and Plant Protection
|
| Street address |
Betty-Heimann-Str. 3
|
| City |
Halle/Saale |
| ZIP/Postal code |
06120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11158 |
| Series (1) |
| GSE25114 |
Genome-wide expression profiling of Fusarium graminearum in response to azole fungicide treatment |
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