|
| Status |
Public on Jan 19, 2011 |
| Title |
Segregant 10b |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Segregant 10b
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: Segregant 10b
genetic background: S288C x 59A
rmax: 2.12
r50: 1.535
r70: 1.24
fd: 89.5
cp: 246.32
nass: 339.3664321
suc: 0.343
gly: 5.7975
ace: 0.881
pyr: 0.12
|
| Growth protocol |
Fermentation experiments and precultures were carried out at 28°C on a 1L synthetic medium MS300 (BELY et al. 1990). Extraction time at 50% of fermentation advancement (45g of released CO2).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Gibco BRL, Life Technologies) (Chomczynski et Sacchi, 1987) and purified using a “RNA Cleanup kit” from Qiagen
|
| Label |
Cy3
|
| Label protocol |
Fluorescent-labelled cDNA was synthesized from 5µg of total RNA using the CleanUP System (Pronto). Labelled cDNA was purified using the Pronto Purification kit (Pronto)
|
| |
|
| Channel 2 |
| Source name |
Pool of the 30 segregants
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: Pool of the 30 segregants
genetic background: S288C x 59A
|
| Growth protocol |
Fermentation experiments and precultures were carried out at 28°C on a 1L synthetic medium MS300 (BELY et al. 1990). Extraction time at 50% of fermentation advancement (45g of released CO2).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Gibco BRL, Life Technologies) (Chomczynski et Sacchi, 1987) and purified using a “RNA Cleanup kit” from Qiagen
|
| Label |
Cy5
|
| Label protocol |
Fluorescent-labelled cDNA was synthesized from 5µg of total RNA using the CleanUP System (Pronto). Labelled cDNA was purified using the Pronto Purification kit (Pronto)
|
| |
|
| |
| Hybridization protocol |
Hybridization was carried out in a hybridization chamber (Corning) and using Pronto Universal Hybridization Kit Quick
|
| Scan protocol |
The hybridization signal was detected with a GenePix 4000B laser Scanner (Axon Instruments), and the signal was transformed to numerical values using the integrated GenePix software version 3.0
|
| Data processing |
initial filtering:mean red signal must be greater than 3 times the mean red background signal print-tip-loess within-array normalization, quantile between-array normalization. R 2.9.2 software and limma bioconductor package used. All gpr files are Cy3 (test) to Cy5 (pool of 30)
|
| |
|
| Submission date |
Jan 04, 2011 |
| Last update date |
Jan 19, 2011 |
| Contact name |
Bruno Blondin |
| E-mail(s) |
bruno.blondin@supagro.inra.fr
|
| Organization name |
INRA
|
| Department |
UMR1083
|
| Lab |
SPO
|
| Street address |
2 place Pierre Viala
|
| City |
Montpellier |
| ZIP/Postal code |
34060 |
| Country |
France |
| |
|
| Platform ID |
GPL11380 |
| Series (1) |
| GSE26437 |
A combined genetic and genomic approach uncovers molecular basis of wine yeast fermentation traits |
|
