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Sample GSM225520 Query DataSets for GSM225520
Status Public on Aug 31, 2007
Title Aerobic nitrogen limited chemostat culture with 79% CO2 D=0.1/h -2
Sample type RNA
 
Source name Steady state Aerobic nitrogen limited chemostat culture with 79% CO2
Organism Saccharomyces cerevisiae
Characteristics The prototrophic S. cerevisiae strain CEN.PK113-7D [18] was used for this study
Biomaterial provider J Aguilera
Treatment protocol Liquid nitrogen quenching
Growth protocol Cells were grown at 30 °C in laboratory fermenters (Applikon, Schiedam, The Netherlands) with a working volume of 1 l as described in . Cultures were fed with a defined synthetic medium that was designed to allow for steady-state growth limited by either carbon or nitrogen, with all other requirements in excess and at a constant residual concentration. The dilution rate was set to 0.10 h−1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2-M KOH with the use of an Applikon ADI 1030 Biocontroler. Stirrer speed was 800 rpm, and the gas flow was 0.5 l min−1.
Synthetic media were prepared as described by Verdyun (1992) with the following modifications: for carbon-limited cultivation, the medium contained 5.0 g l−1 of (NH4)2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and either 7.5 g l−1 of glucose or 5.76 g l−1 of ethanol. For nitrogen-limited cultures, 1.0 g l−1 of (NH4)2SO4, 5,3 g l−1 of K2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and the necessary glucose to keep the residual glucose concentration at 18 g l−1 (59 and 62.2 g l−1 for the CO2-untreated and -treated cultures, respectively). This was done to avoid differences in the degree of glucose repression.
For CO2-enriched aerobic cultivation, cultures were sparged with a defined gas mixture containing 79% CO2 and 21% O2 (HoekLoos, Schiedam, The Netherlands).
Extracted molecule total RNA
Extraction protocol One hundred millilitres of culture was sampled directly from the fermentor into a beaker containing 200–300 ml of liquid nitrogen and then processed . Total RNA was extracted with phenol/chloroform. mRNA extraction, cDNA synthesis and labelling, as well as array hybridisation against Affymetrix YG-S98 GeneChips® was performed as described in the Affymetrix user’s manual. Data acquisition was performed using the software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0 (Affymetrix, Santa Clara, CA, USA).
Label Biotinylated dUTP - streptavidine Phycoerythrin (SAPE)
Label protocol One hundred millilitres of culture was sampled directly from the fermentor into a beaker containing 200–300 ml of liquid nitrogen and then processed . Total RNA was extracted with phenol/chloroform. mRNA extraction, cDNA synthesis and labelling, as well as array hybridisation against Affymetrix YG-S98 GeneChips® was performed as described in the Affymetrix user’s manual. Data acquisition was performed using the software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0 (Affymetrix, Santa Clara, CA, USA).
 
Hybridization protocol One hundred millilitres of culture was sampled directly from the fermentor into a beaker containing 200–300 ml of liquid nitrogen and then processed . Total RNA was extracted with phenol/chloroform. mRNA extraction, cDNA synthesis and labelling, as well as array hybridisation against Affymetrix YG-S98 GeneChips® was performed as described in the Affymetrix user’s manual. Data acquisition was performed using the software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0 (Affymetrix, Santa Clara, CA, USA).
Scan protocol One hundred millilitres of culture was sampled directly from the fermentor into a beaker containing 200–300 ml of liquid nitrogen and then processed . Total RNA was extracted with phenol/chloroform. mRNA extraction, cDNA synthesis and labelling, as well as array hybridisation against Affymetrix YG-S98 GeneChips® was performed as described in the Affymetrix user’s manual. Data acquisition was performed using the software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0 (Affymetrix, Santa Clara, CA, USA).
Description J05
Data processing MAS5.0 calculated intensity with global array targetting at 150
 
Submission date Aug 29, 2007
Last update date Aug 14, 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 (2)
GSE8900 Genome-wide transcriptional responses of Saccharomyces cerevisiae to high carbon dioxide concentrations
GSE11452 Saccharomyces cerevisiae chemostat steady state microarray compendium

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-MurIL2_at 4.0 A 0.760937
AFFX-MurIL10_at 0.2 A 0.932322
AFFX-MurIL4_at 0.2 A 0.976071
AFFX-MurFAS_at 0.4 A 0.916408
AFFX-BioB-5_at 50.0 P 0.001410
AFFX-BioB-M_at 55.7 P 0.000081
AFFX-BioB-3_at 44.6 P 0.000446
AFFX-BioC-5_at 61.6 P 0.000169
AFFX-BioC-3_at 58.8 P 0.000081
AFFX-BioDn-5_at 71.2 P 0.000044
AFFX-BioDn-3_at 423.5 P 0.000044
AFFX-CreX-5_at 1024.6 P 0.000044
AFFX-CreX-3_at 1317.6 P 0.000044
AFFX-BioB-5_st 0.6 A 0.712274
AFFX-BioB-M_st 2.3 A 0.659352
AFFX-BioB-3_st 1.0 A 0.772364
AFFX-BioC-5_st 1.6 A 0.737173
AFFX-BioC-3_st 0.7 A 0.659352
AFFX-BioDn-5_st 2.7 A 0.659339
AFFX-BioDn-3_st 6.4 M 0.050229

Total number of rows: 9335

Table truncated, full table size 225 Kbytes.




Supplementary file Size Download File type/resource
GSM225520.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM225520.EXP.gz 519 b (ftp)(http) EXP
Processed data included within Sample table

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