 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 30, 2008 |
| Title |
Transcriptional responses to lactic acid in anaerobic chemostat cultures of Saccharomyces cerevisiae |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by array
|
| Summary |
Raw expression values (CHP data) for transcriptional profiling of the response of Saccharomyces cerevisiae to challenges with lactic acid at pH 3 and pH 5.
Keywords: response to lactic acid
|
| |
|
| Overall design |
The laboratory reference strain CEN.PK 113-7D (MATa) was grown at 30 °C in 1.5-L chemostat fermentors (Applikon, Schiedam, The Netherlands) with a working volume of 1-L using an electronic level sensor to maintain a constant volume. All cultures, including the reference, were fed with minimal medium as described by Verduyn et al. (1992) with 25 g L-1 glucose as the limiting nutrient and 0.15 ml L-1 silicone antifoam (BDH, Poole, England) to prevent excessive foaming. The dilution rate was set to 0.10 h-1 and the pH was controlled at 5.0 with the automatic addition (ADI 1031 bio controller, Applikon) of 2 M KOH. The stirrer speed was set at 800 RPM and anaerobicity was maintained by sparging the fermentor with N2 gas at 500 ml min-1. To prevent diffusion of oxygen, the fermentor was equipped with Norprene tubing and Viton O-rings and the medium vessel was also flushed with N2 gas. A comparable degree of weak acid uncoupling was ensured by decreasing the biomass yield to approximately 50% of the reference condition (no organic acids added) with the addition of the appropriate concentration of lactic acid to the reservoir media.
Sampling of chemostat cultures, probe preparation and hybridization to Affymetrix GeneChip microarrays was performed as described previously (Piper et al., 2002), but with the following modifications. Double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix). The double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix). Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA.
Data acquisition was performed using the Affymetrix scanner 3000, quantification of array images and data filtering were performed with the Affymetrix software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0.
|
| |
|
| Contributor(s) |
Abbott DA, Suir E, Pronk JT, van Maris AJ |
| Citation(s) |
18676708 |
| |
| Submission date |
Jan 04, 2008 |
| Last update date |
Jul 01, 2016 |
| Contact name |
Jean-Marc Daran |
| E-mail(s) |
[email protected]
|
| Phone |
+31 15 278 2412
|
| Organization name |
Delft University of Technology
|
| Department |
Department of Biotechnology
|
| Lab |
Kluyver centre for genomics of industrial organisms
|
| Street address |
Julianalaan 67
|
| City |
Delft |
| ZIP/Postal code |
2628BC |
| Country |
Netherlands |
| |
|
| Platforms (1) |
| GPL90 |
[YG_S98] Affymetrix Yeast Genome S98 Array |
|
| Samples (12)
|
| GSM137497 |
C-lim Anaerobic reference (pH 5) #1 |
| GSM137498 |
C-lim Anaerobic reference (pH 5) #2 |
| GSM137675 |
C-lim Anaerobic reference (pH 5) #3 |
| GSM254433 |
C-lim anaerobic reference (pH 3) #1 |
| GSM254434 |
C-lim anaerobic reference (pH 3) #2 |
| GSM254435 |
C-lim anaerobic reference (pH 3) #3 |
| GSM254436 |
C-lim anaerobic 500 mM lactic acid (pH 3) #1 |
| GSM254438 |
C-lim anaerobic 500 mM lactic acid (pH 3) #2 |
| GSM254443 |
C-lim anaerobic 500 mM lactic acid (pH 3) #3 |
| GSM254444 |
C-lim anaerobic 900 mM lactic acid (pH 5) #1 |
| GSM254445 |
C-lim anaerobic 900 mM lactic acid (pH 5) #2 |
| GSM254446 |
C-lim anaerobic 900 mM lactic acid (pH 5) #3 |
|
| Relations |
| BioProject |
PRJNA108171 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE10066_RAW.tar |
17.6 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...