|
| Status |
Public on Jan 17, 2013 |
| Title |
AAP strain_anaerobic conditions_biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Saccharomyces cerevisiae strain with less amyalse productions at anaerobic batch fermentations
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: CEN. PK 530-1C with pTEF1-alpha factor leader amylase (2 μm POT1)
|
| Treatment protocol |
Samples for microarray analysis were taken at approximatly OD=1, and centrifuged at 4 degree for 3min, depleted supernatant, and stored in liquid nitrogen for short time and stored at -80 °C until processing
|
| Growth protocol |
All fermentations were performed in DasGip 1.0-liter stirrer-pro vessels (Drescher Amold Schneider, Germany) with a working volume of 500ml of SD-SCAA media, at 30°C, 600 rpm agitation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Minikit (Qiagen) and processed to cRNA using the Genechip 3’ IVT Express Kit (Affymetrix) and hybridized/scanned on the Yeast Genome 2.0 Array (Affymetrix) to create CEL files.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 7.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from AAP strain_anaerobic conditions_biological rep3
|
| Data processing |
Images were analyzed using R 2.10.1 software and Bioconductor packages. Briefly, data normalization was carried out using the method of Probe Logarithmic Intensity Error (PLIER) with perfect match probe only (PM-only).
|
| |
|
| Submission date |
Jun 21, 2012 |
| Last update date |
Jan 17, 2013 |
| Contact name |
Tobias Österlund |
| E-mail(s) |
tobiaso@chalmers.se
|
| Organization name |
Chalmers University of Technology
|
| Department |
Dept. of Chemical and Biological Engineering
|
| Lab |
Systems biology
|
| Street address |
Kemivägen 10
|
| City |
Göteborg |
| ZIP/Postal code |
41296 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL2529 |
| Series (1) |
| GSE38848 |
Expression data from Saccharomyces cerevisiae |
|
