|
| Status |
Public on May 23, 2008 |
| Title |
C-lim Anaerobic reference (pH 5) #3 |
| Sample type |
RNA |
| |
|
| Source name |
Chemostat sample
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Saccharomyces cerevisiae CEN.PK 113-7D (MATa)
|
| Biomaterial provider |
D. Abbott
|
| Treatment protocol |
N2 quenching
|
| Growth protocol |
The laboratory reference strain CEN.PK 113-7D (MATa) was grown at 30 °C in 2-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.
Verduyn C, Postma E, Scheffers WA & van Dijken JP (1992) Effect of benzoic acid on metabolic fluxes in yeast: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-517.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sampling of chemostat cultures and probe preparation was performed as described previously (Piper et al., 2002).
Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008.
|
| Label |
biotin
|
| Label protocol |
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.
Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008.
|
| |
|
| Hybridization protocol |
According to manufacturer's procedures
|
| Scan protocol |
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.
|
| Description |
C-lim Anaerobic reference (pH 5) #3
DA18E
|
| Data processing |
Chip file GCOS (Affymetrix - version 1.2.0.037)
|
| |
|
| Submission date |
Sep 28, 2006 |
| Last update date |
Sep 23, 2009 |
| 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 |
| |
|
| Platform ID |
GPL90 |
| Series (7)
|
| GSE5926 |
Transcriptional response to weak organic acids in chemostat cultures of Saccharomyces cerevisiae |
| GSE10066 |
Transcriptional responses to lactic acid in anaerobic chemostat cultures of Saccharomyces cerevisiae |
| GSE11452 |
Saccharomyces cerevisiae chemostat steady state microarray compendium |
| GSE15094 |
Resistance to hop iso-α-acids in yeast involves active export and vacuolar sequestration |
| GSE15465 |
The regulation of reserve carbohydrate metabolism in S cerevisiae in response to nutrient availability |
| GSE18128 |
Involvement of Snf7 and Rim101 in regulation of TIR1 and anaerobically up-regulated genes in yeast |
| GSE30535 |
Engineering topology and kinetics of sucrose metabolism in Saccharomyces cerevisiae for improved ethanol yield |
|
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