|
| Status |
Public on Mar 21, 2014 |
| Title |
Umaydis_glucose_oil |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
U. maydis grown with oil
|
| Organism |
Ustilago maydis 521 |
| Characteristics |
strain: UM521
|
| Growth protocol |
The strains were grown in the medium (0.03% MgSO4, 0.03% KH2PO4, 0.1% yeast extract, pH 6.0 containing 5% soybean oil or 10% glucose), at 25 °C on a rotary shaker (300 rpm) for 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using ISOGEN (Wako). mRNA was purified from approximately 0.2 mg total RNA using an OligotexTM-dT30 <Super> mRNA Purification kit (Takara, Shiga, Japan)
|
| Label |
Cy3,Cy5
|
| Label protocol |
Two cDNA samples labeled with Cy5 and Cy3 for each were mixed and applied onto Nimblegen Gene Expression Arrays (Roche Diagnostics, Tokyo)
|
| |
|
| Channel 2 |
| Source name |
U. maydis grown with glucose
|
| Organism |
Ustilago maydis 521 |
| Characteristics |
strain: UM521
|
| Growth protocol |
The strains were grown in the medium (0.03% MgSO4, 0.03% KH2PO4, 0.1% yeast extract, pH 6.0 containing 5% soybean oil or 10% glucose), at 25 °C on a rotary shaker (300 rpm) for 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using ISOGEN (Wako). mRNA was purified from approximately 0.2 mg total RNA using an OligotexTM-dT30 <Super> mRNA Purification kit (Takara, Shiga, Japan)
|
| Label |
Cy5,Cy3
|
| Label protocol |
Two cDNA samples labeled with Cy5 and Cy3 for each were mixed and applied onto Nimblegen Gene Expression Arrays (Roche Diagnostics, Tokyo)
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol.
|
| Scan protocol |
The slide was scanned to measure the fluorescence intensity of the two fluorophores using a GenePix 4200A scanner (Axon Instruments at Molecular Devices, Sunnyvale, CA).
|
| Data processing |
The raw data (.pair files) of two dyes were merged and processed using R-BioConductor package. Two-color data with dye swap experiments were normalized and analyzed by limma module. Data was normalized by setting the baseline measurement per spot and per segment of the chip via intensity dependent (LOESS) normalization with dye swap experiment using the limma module.
|
| |
|
| Submission date |
May 22, 2013 |
| Last update date |
Mar 21, 2014 |
| Contact name |
Hideaki Koike |
| E-mail(s) |
hi-koike@aist.go.jp
|
| Phone |
+81-29-861-6679
|
| Organization name |
National Institute of Advanced Industrial Science and Technology
|
| Street address |
Higashi 1-1-1
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-0025 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17185 |
| Series (1) |
| GSE47171 |
Expression analysis of Pseudozyma antarctica T-34 and Ustilago maydis on different carbon source |
|
