|
| Status |
Public on Dec 21, 2011 |
| Title |
IMW004 lactate batch -1 (MA153) |
| Sample type |
RNA |
| |
|
| Source name |
20 g.l aerobic lactate batch
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: IMW004
growth condition: ethanol-limited chemostatsteady state at time point 200h
|
| Treatment protocol |
Yeast cells were collected by rapid filtration (Belinchón et al 2004) and stored at -70 oC until use
|
| Growth protocol |
Aerobic batch cultures for transcriptome analysis were carried out at 30oC in 2 litre laboratory fermentors (Applikon, Schiedam, The Netherlands) with a working volume of 1 litre. Synthetic medium [1] was supplemented with 20 g·l-1 lactic acid (Fluka 09578) as sole carbon source. The pH of this medium was set to 5.0 before autoclaving (120oC). Antifoam Emulsion C (Sigma, St. Louis, USA) was autoclaved separately (120 ºC) as a 20% (w/v) solution and added to a final concentration of 0.2 g·l-1. The culture pH was maintained at 5.0 by automatic addition of 2 M KOH and 2 M H2SO4. Cultures were stirred at 800 rpm and sparged with 500 ml air·min-1. The precultures were grown on ethanol as described above. Six hours before inoculation of the batch cultures, 25 mM lactate was added to the preculture to induce lactate metabolism. [1] Verduyn C, Postma E, Scheffers WA, Van Dijken JP: Effect of benzoic acid on metabolic fluxes in yeasts: A continuous culture study on the regulation of respiration and alcoholic fermentation. Yeast 1992, 8(7):501-517.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA to be used for the microarrays was extracted using the hot-phenol method
|
| Label |
biotin
|
| Label protocol |
cDNA synthesis, cRNA synthesis and labelling, as well as array hybridization were performed as described (De Nicola et al 2007 AEM,73, 7680-7692 )
|
| |
|
| Hybridization protocol |
Acquisition and quantification of the Affymetrix yeast S98 array images as well as primary data analysis were performed using the Affymetrix GeneChip Operating Software (GCOS) 2.1.
|
| Scan protocol |
Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions
|
| Description |
ethanol-limited chemostatsteady state at time point 200h
|
| Data processing |
Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity was scaled to 150.
|
| |
|
| Submission date |
Aug 24, 2011 |
| Last update date |
Dec 21, 2011 |
| Contact name |
Jean-Marc Daran |
| E-mail(s) |
j.g.daran@tudelft.nl
|
| 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 (1) |
| GSE31634 |
Laboratory evolution of Jen1p-independent lactate transport in Saccharomyces cerevisiae: identification of ADY2 alleles by whole genome resequencing and mRNA expression analysis |
|
