|
| Status |
Public on Mar 01, 2012 |
| Title |
DK21_minus_36h_2 |
| Sample type |
RNA |
| |
|
| Source name |
Fusarium graminearum virus free at 36 h
|
| Organism |
Fusarium graminearum |
| Characteristics |
anamorph: Fusarium graminearum
cell type: hyphae
|
| Treatment protocol |
There is no special treatment in F. graminearum.
|
| Growth protocol |
Virus-free and FgV1-DK21-infected F. graminearum strains were maintained on potato dextrose agar (PDA) at 25°C with 12 h light–dark cycle. Freshly grown mycelia from PDA media plate were inoculated in 50 or 200 ml of complete media (CM) broth and incubated at 25°C for 36 hrs or 120 hrs in an orbital shaker (150 rpm). Hyphae were collected by filtering through 3MM paper, washed with distilled water, dried by blotting with paper towels and frozen at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen mycelia were pulverized with mortar and pestle using liquid nitrogen for nucleic acid extraction. Total RNAs were extracted by Iso-RNA Lysis reagent (5 PRIME, Germany). Extracted total RNA was treated with DNase I (Takara, Japan) to remove genomic DNA according to instructions provided by the manufacturer. The total RNA sample were precipitated with ethanol and resuspended in DEPC-treated water finally.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of wild-type Fusarium graminearum. It is the second of three wild-type biological replicates used in this experiment and is harvested together with virus infected samples at 36 hrs.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Jul 11, 2011 |
| Last update date |
Mar 01, 2012 |
| Contact name |
Won Kyong Cho |
| E-mail(s) |
wonkyong@gmail.com
|
| Phone |
+82-2-880-4928
|
| Organization name |
Seoul National University
|
| Department |
Department of Agricultural Biotechnology and Center for Fungal Pathogenesis
|
| Street address |
5103-ho, 200-dong, Daehak-dong, Kwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
151-921 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13843 |
| Series (1) |
| GSE30545 |
Genome-wide expression profiling reveals transcriptional reprogramming in Fusarium graminearum by FgV1-DK21 virus infection |
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