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Sample GSM254433 Query DataSets for GSM254433
Status Public on Jul 30, 2008
Title C-lim anaerobic reference (pH 3) #1
Sample type RNA
 
Source name Chemostat sample
Organism Saccharomyces cerevisiae
Characteristics Saccharomyces cerevisiae CEN.PK 113-7D (MATa)
Biomaterial provider D. Abbott
Treatment protocol Quenching in ice-cold TRIS-EDTA (pH 8)
Growth protocol 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 3.0 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), but quenching was performed in ice-cold TRIS-EDTA rather than liquid nitrogen. Cultures were quenched in ice-cold TRIS-EDTA (TE) buffer at pH 8 (5 times the volume of sample (5x volume)), then washed in ice-cold TE buffer (2x volume) followed by ice-cold demi-water (2x volume).
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 SAPE
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 3) #1
Data processing Chip file GCOS (Affymetrix - version 1.2.0.037)
 
Submission date Jan 04, 2008
Last update date May 22, 2008
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)
GSE10066 Transcriptional responses to lactic acid in anaerobic chemostat cultures of Saccharomyces cerevisiae

Data table header descriptions
ID_REF
VALUE Signal value
ABS_CALL presence call
DETECTION P-VALUE detection p-value

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-MurIL2_at 1.00535 A 0.98333
AFFX-MurIL10_at 0.36678 A 0.98333
AFFX-MurIL4_at 0.248714 A 0.99156
AFFX-MurFAS_at 2.62317 A 0.631562
AFFX-BioB-5_at 37.6135 P 0.00179591
AFFX-BioB-M_at 59.5752 P 0.000195116
AFFX-BioB-3_at 51.0312 P 7.00668e-05
AFFX-BioC-5_at 126.391 P 4.42873e-05
AFFX-BioC-3_at 165.438 P 4.42873e-05
AFFX-BioDn-5_at 351.883 P 4.42873e-05
AFFX-BioDn-3_at 855.437 P 4.42873e-05
AFFX-CreX-5_at 1527.86 P 4.42873e-05
AFFX-CreX-3_at 1894.11 P 4.42873e-05
AFFX-BioB-5_st 0.807006 A 0.883887
AFFX-BioB-M_st 2.80759 A 0.749204
AFFX-BioB-3_st 1.30316 A 0.868639
AFFX-BioC-5_st 4.15949 A 0.631562
AFFX-BioC-3_st 4.87543 A 0.51489
AFFX-BioDn-5_st 2.81919 A 0.631562
AFFX-BioDn-3_st 18.3414 P 0.0309764

Total number of rows: 9335

Table truncated, full table size 267 Kbytes.




Supplementary file Size Download File type/resource
GSM254433.CEL.gz 1.2 Mb (ftp)(http) CEL
GSM254433.CHP.gz 54.2 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data provided as supplementary file
Processed data included within Sample table

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