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Series GSE3021 Query DataSets for GSE3021
Status Public on Jan 01, 2006
Title Six diploid strains grown in four conditions
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary Six strains of Saccharomyces cerevisiae were grown in four different environments representing a continuum of rich and poor natural conditions
Keywords: Stress response, genetic diversity
 
Overall design Some hybridizations were performed in duplicates on the same microarrays. Two complete sets of PCR products were printed on the same glass slide and under a single cover slip. These duplicates are labeled Array_A and Array_B. Since these are not complete technical replicates, they were averaged in Landry et al. (Gene, accepted) following the normalization and prior to statistical analysis.Replicate indicates a complete independent hybridization.
Strains were grown in YPD (laboratory conditions), synthetic wine must (SWM) simulating fermentation conditions, or in low-nitrogen, proline-supplemented SWM (SWM_NS). The standard nutrient medium for yeast cultivation (YPD) is composed of 1% yeast extract, 2% peptone, and 2% dextrose. SWM contains 0.17% yeast nitrogen base, without amino acids and (NH4)SO4, 0.15% casamino acids, 0.05% NH4Cl, 0.60% DL-malic acid, 0.02% citric acid, 0.15% L-tartaric acid, 21% glucose, and 0.20% anaerobic factors ergosterol–Tween 80 (total 10 mg/L ergosterol, 0.5 ml/L Tween 80). The pH was adjusted to 3.3 with KOH. SWM has a total nitrogen concentration of 247.2 mg/L. The nitrogen starvation medium (SWM_NS) was composed of 0.17% yeast nitrogen base, 0.1% L-proline, 0.60% DL-malic acid, 0.02% citric acid, 0.15% L-tartaric acid, 21% glucose, and 0.20% ergosterol Tween 80 (10 mg/L ergosterol, 0.5 ml/L Tween 80). The pH was adjusted to 3.3. SWM_NS has a total nitrogen concentration of 123 mg/L. All cells were grown at 28°C. For YPD, cells were grown aerobically in a shaker at 200 rpm and harvested at an optical density (OD) of 0.8 (A600). SWM and SWM_NS: Strains were grown aerobically overnight in SWM. Cells were then diluted to 0.2 OD in SWM and left to grow to 0.8 OD in a shaker at 50 rpm. Anaerobic conditions were established by locked fermentation flasks with CO2 outlets filled with water. For growth under nitrogen starvation, cells were then pelleted (3000 g, 5 min), washed with sterile water, resuspended in SWM_NS medium, and left to grow for 4 (NS_4) or 24 (NS_24) hours under the same conditions. For all conditions, cells were harvested by centrifugation (3000 g, 10 min) at then flash frozen using liquid nitrogen. The hybridization protocol is described in Townsend et al. (2003). Hybridization Spots were visually inspected and flawed ones were flagged (negative values).
 
Citation(s) 16427747
Submission date Jul 27, 2005
Last update date Mar 16, 2012
Contact name Duccio Cavalieri
E-mail(s) duccio.cavalieri@unifi.it
Phone 39.055.4271327
Fax 39.055.4271280
Organization name University of Florence
Department Department of Pharmacology
Street address Viale Pieraccini 6
City Florence
ZIP/Postal code 50139
Country Italy
 
Platforms (1)
GPL2682 Yeast ORF array Bauer Center for Genomics Research Harvard University, Cavalieri Lab
Samples (91)
GSM66246 Saccharomyces cerevisiae BY4743 YPD EM93 YPD Array_A
GSM66247 Saccharomyces cerevisiae BY4743 YPD EM93 YPD Array_B
GSM66248 Saccharomyces cerevisiae BY4743 YPD EM93 YPD Replicate1_Array_A
Relations
BioProject PRJNA93205

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