|
| Status |
Public on Sep 01, 2006 |
| Title |
Sigma1278b_thrVSurea_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Sigma1278b ; minimum medium ; NS = threonine
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Strain=Sigma1278b
|
| Growth protocol |
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = threonine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)
|
| Extracted molecule |
polyA RNA |
| Label |
Cy5
|
| |
|
| Channel 2 |
| Source name |
Sigma1278b ; minimum medium ; NS = urea
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Strain=Sigma1278b
|
| Growth protocol |
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = urea (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)
|
| Extracted molecule |
polyA RNA |
| Label |
Cy3
|
| |
|
| |
| Scan protocol |
The hybridized microarray was scanned with a GMS418 fluorescence reader (Genetic MicroSystems, Woburn, MA) having a resolution of 10 µm; the laser power was set at 100%. The slide was scanned twice to get the Cy5 and Cy3 signals, once with the PMT (Photo Multiplier Tube) gain set at 80% and once with it set at 20%. Signal quantification for each probe on the microarray was performed with GenePix 4.01.17 image acquisition software (Axon Instruments, Union City, CA). Spots with a diameter greater than 210 µm or smaller than 80 were considered low-quality spots as were spots having (median pixel intensity - mean pixel intensity)> 40% of the median pixel intensity for each channel and spots having less than 95% of their spot pixels more than two standard deviations above background in either the green or the red channel. Low-quality spots were excluded from further analysis.
|
| Description |
comparison of Sigma1278b transcriptome during growth on threonine and on urea.
|
| Data processing |
Intensity values from high-PMT-gain pictures were used, except in the case of saturated spots. In the latter case, intensity values from low-PMT-gain pictures were used after scale correction. Intensity-dependent within-tip-group and scale normalization were applied as described by Yang et al. 2002 (PMID = 11842121) using Bioconductor tools (Gentleman et al. 2004 : PMID = 15461798). Fluorescence ratios were computed on the basis of hybridization signals normalized with background corrections.
|
| |
|
| Submission date |
May 17, 2006 |
| Last update date |
May 18, 2006 |
| Contact name |
Patrice Godard |
| Organization name |
Université Libre de Bruxelles
|
| Department |
IBMM
|
| Lab |
Physiologie Moléculaire de la Cellule
|
| Street address |
rue des professeurs Jeener et Brachet, 12
|
| City |
gosselies |
| ZIP/Postal code |
6041 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL3774 |
| Series (1) |
| GSE4861 |
Effect of twenty-one different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae |
|
