|
| Status |
Public on Feb 11, 2011 |
| Title |
SOK2 overexpressing yeast, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Yeast VIN13 overexpressing transcription factor SOK2 at day2 of fermentation
|
| Organism |
Saccharomyces cerevisiae Vin13 |
| Characteristics |
genotype: SOK2 overexpressing
time: day 2 of alcholic fermentation
replicate: 2
|
| Treatment protocol |
Cells were harvested by brief centrifugation and washed prior to extraction.
|
| Growth protocol |
Yeast were inoculated at an OD600 of 0.1 in synthetic wine must in microaerobic fermentation vials. Fermentation was carried out at room temperature.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted as described using a modified hot-phenol method as described by Abbott et al (2007).
|
| Label |
biotin
|
| Label protocol |
Following second strand cDNA synthesis (starting material 100ng of total RNA), biotinylated cRNA was prepared in accordance with the Affymetrix 3' Expression protocol . The expected profile of amplified RNA should be in the range of 250 -5500nt with most of the amplified RNA appearing in the 600-12--nt range. 7.5ug of amplified RNA is required for hybridisation to an array.
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 ug of labelled fragmented amplified RNA was hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
The GeneChips were scanned using the Affymetrix GeneChip® 3000 Scanner 7G. AGCC is used for image acquisition.
|
| Data processing |
The cell intensity data was analyzed in Affymetrix Expression Console using the RMA algorithm. The RMA workflow is quantile normalisation with general background correction.
|
| |
|
| Submission date |
Jan 28, 2011 |
| Last update date |
Feb 11, 2011 |
| Contact name |
Debra Rossouw |
| E-mail(s) |
debra@sun.ac.za
|
| Organization name |
University of Stellenbosch
|
| Department |
Institute for Wine Biotechnology
|
| Lab |
Yeast
|
| Street address |
Cnr Neethling and Victoria rd
|
| City |
Stellenbosch |
| State/province |
Western Cape |
| ZIP/Postal code |
7600 |
| Country |
South Africa |
| |
|
| Platform ID |
GPL2529 |
| Series (1) |
| GSE26929 |
Expression data from yeast strain VIN13 overexpressing the transcription factor SOK2 |
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