|
| Status |
Public on Jan 01, 2010 |
| Title |
cold 10degC 2h |
| Sample type |
RNA |
| |
|
| Source name |
yeast culture in liquid medium
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
temperature: 10degC
time: 2h
|
| Treatment protocol |
Samples were kept at -80°C until RNA extraction.
|
| Growth protocol |
Yeast cells of the strain S288C were grown in SD-Medium under optimal conditions of 28°C until they reached a OD600 of 1, afterwards cultures were shifted to ambient temperatures of 37°C, 10°C as well as kept at 28°C; a time series of 8 time points in a range of 24 hours was collected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For extraction of total RNA the MasterPure™ Yeast RNA Purification Kit (Epicentre Biotechnologies, Madison, Wisconsin, USA) was used. Subsequent RNA clean-up was performed using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany).
|
| Label |
Biotin
|
| Label protocol |
Control and cold samples: cDNA synthesis and in vitro-transcription was done with Ambion´s Message Amp II Kit (Cat. No. 1751). Heat Samples: cDNA synthesis and in vitro-transcription was done with Roche´s Microarray Target Amplification Kit (Cat No 3310191), in combination with Standard-in vitro-transcription with the Message Amp II Kit (#1751) from Ambion.
|
| |
|
| Hybridization protocol |
Hybridization solution was prepared according to Affymetrix´ GeneChip Expression Analysis Technical Manual. The final concentration of cRNA is 60 ng/µl. Spike-in controls: pre-labelled cRNAs (Affymetrix, Cat. No. 900454) are spiked in at defined concentrations: - bioB: 1.5 pM; - bioC: 5 pM; - bioD: 25 pM; - cre: 100 pM. Hybridization was performed for 16-18 hours at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).
|
| Scan protocol |
GeneChip Scanner 3000 7G (Affymetrix) controlled by Affymetrix´ software GeneChip Operating System (GCOS). Primary data analysis was performed with Affymetrix´ software GeneChip Operating System (GCOS).
|
| Description |
none
|
| Data processing |
probeset quantile normalization (Bioconductor, cerevisiae probes), RMA (RMAExpress, pombe probes)
|
| |
|
| Submission date |
Mar 23, 2009 |
| Last update date |
Nov 23, 2009 |
| Contact name |
Dirk Walther |
| E-mail(s) |
walther@mpimp-golm.mpg.de
|
| Phone |
49-331-5678108
|
| Organization name |
Max Planck Institute for Molecular Plant Physiology
|
| Department |
Bioinformatics
|
| Street address |
Am Mühlenberg 1
|
| City |
Potsdam-Golm |
| ZIP/Postal code |
14476 |
| Country |
Germany |
| |
|
| Platform ID |
GPL2529 |
| Series (1) |
| GSE15352 |
Dynamic transcriptional and metabolic responses in yeast adapting to temperature stress. |
|
