1 sample(s) found by the keyword GSM225463.


  1. GEO sample ID: GSM225463
    • Sample_geo_accession: GSM225463
    • Sample_status: Public on Aug 31 2007
    • Sample_submission_date: Aug 29 2007
    • Sample_last_update_date: Aug 30 2007
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Prolongued aerobic maltose limited chemostat culture 45 generations old
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: The haploid, prototrophic S. cerevisiae strain CEN.PK113-7D (MATa MAL2-8c SUC2) was obtained from Dr P. Ko¨tter, Frankfurt, Germany. Precultures were grown to stationary phase in shake-flask cultures of synthetic medium (Verduyn et al., 1992), adjusted to pH 6?0 and containing 2% (w/v) glucose. After adding sterile glycerol (30 %, v/v), 2 ml aliquots were stored in sterile vials at 280 uC. These frozen stock cultures were used to inoculate precultures for chemostat cultivation.
    • Sample_characteristics_ch1: Verduyn, C., Postma, E., Scheffers, W. A. & van Dijken, J. P. (1992). Effect of benzoic acid on metabolic fluxes in yeasts: a continuous study on regulation of respiration and alcoholic fermentation. Yeast 8, 501-517.
    • Sample_biomaterial_provider_ch1: MLA Jansen
    • Sample_treatment_protocol_ch1: Liquid nitrogen quenching
    • Sample_growth_protocol_ch1: Aerobic chemostat cultivation was performed at a dilution rate of 0.10 h−1 at 30°C in 2.0-liter laboratory fermentors (Applikon, Schiedam, The Netherlands) with stirring at 800 rpm. The working volume of the cultures was kept at 1.0 liter by a peristaltic effluent pump coupled to an electrical level sensor. This setup ensured that under all growth conditions, biomass concentrations in samples taken directly from the culture differed by <1% from biomass concentrations in samples taken from the effluent line. The exact working volume was measured after each experiment. The pH was kept at 5.0 ± 0.1 by an ADI 1030 biocontroller via the automatic addition of 2 mol of KOH · liter−1. The fermentor was flushed with air at a flow rate of 0.5 liter · min−1 by using a Brooks 5876 mass flow controller. The dissolved oxygen concentration was continuously monitored with an oxygen electrode (model 34 100 3002; Ingold) and remained above 60% of air saturation. A steady state was defined as the situation in which at least five volume changes had passed after the last change in growth conditions and in which the biomass concentration and the specific rates of carbon dioxide production and oxygen consumption had remained constant (<2% variation) over two volume exchanges. In case of spontaneous oscillatory behavior, a pulse of ethanol (50 mM) was added to the culture to dampen out the oscillations. Chemostat cultures were routinely checked for purity by phase-contrast microscopy.
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Cells were rapidly (within 3 s) transferred
    • Sample_extract_protocol_ch1: from the chemostat culture into liquid nitrogen to immediately
    • Sample_extract_protocol_ch1: quench the metabolism. The frozen cell suspension (about 40 g cell
    • Sample_extract_protocol_ch1: broth) was thawed gently on ice. After complete thawing, the cell
    • Sample_extract_protocol_ch1: suspension was centrifuged at 0 uC, 5000 g, for 5 min. Total RNA
    • Sample_extract_protocol_ch1: extraction from the pellets was performed using the hot-phenol
    • Sample_extract_protocol_ch1: method
    • Sample_label_ch1: Biotinylated dUTP - streptavidine Phycoerythrin (SAPE)
    • Sample_label_protocol_ch1: The results for each growth condition were derived from three independently cultured replicates. Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays, as well as data acquisition and analysis, were performed as previously described (Daran-Lapujade et al., 2004; Piper et al., 2002).
    • Sample_label_protocol_ch1: Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277, 37001–37008.
    • Sample_label_protocol_ch1: Daran-Lapujade, P., Jansen, M. L., Daran, J. M., Van Gulik, W., de Winde, J. H. & Pronk, J. T. (2004). Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae: a chemostat culture study. J Biol Chem 279, 9125–9138.
    • Sample_hyb_protocol: The results for each growth condition were derived from three independently cultured replicates. Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays, as well as data acquisition and analysis, were performed as previously described (Daran-Lapujade et al., 2004; Piper et al., 2002).
    • Sample_hyb_protocol: Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277, 37001–37008.
    • Sample_hyb_protocol: Daran-Lapujade, P., Jansen, M. L., Daran, J. M., Van Gulik, W., de Winde, J. H. & Pronk, J. T. (2004). Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae: a chemostat culture study. J Biol Chem 279, 9125–9138.
    • Sample_scan_protocol: The results for each growth condition were derived from three independently cultured replicates. Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays, as well as data acquisition and analysis, were performed as previously described (Daran-Lapujade et al., 2004; Piper et al., 2002).
    • Sample_scan_protocol: Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277, 37001–37008.
    • Sample_scan_protocol: Daran-Lapujade, P., Jansen, M. L., Daran, J. M., Van Gulik, W., de Winde, J. H. & Pronk, J. T. (2004). Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae: a chemostat culture study. J Biol Chem 279, 9125–9138.
    • Sample_description: M19
    • Sample_data_processing: MAS5.0 calculated intensity with global array targetting at 150
    • Sample_platform_id: GPL90
    • Sample_contact_name: Jean-Marc,,Daran
    • Sample_contact_email: j.g.daran@tudelft.nl
    • Sample_contact_phone: +31 15 278 2412
    • Sample_contact_fax: +31 15 278 23 55
    • Sample_contact_laboratory: Kluyver centre for genomics of industrial organisms
    • Sample_contact_department: Department of Biotechnology
    • Sample_contact_institute: Delft University of Technology
    • Sample_contact_address: Julianalaan 67
    • Sample_contact_city: Delft
    • Sample_contact_zip/postal_code: 2628BC
    • Sample_contact_country: Netherlands
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM225nnn/GSM225463/GSM225463.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM225nnn/GSM225463/GSM225463.EXP.gz
    • Sample_series_id: GSE8897
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Prologued aerobic glucose limited chemostat culture D=0.1/h - 1
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at -13.0 -1.7 A
    AFFX-MurIL10_at -0.8 0.9 A
    AFFX-MurIL4_at 0.1 -0.0 A
    AFFX-MurFAS_at 1.2 -0.5 A
    AFFX-BioB-5_at 292.8 249.8 P
    AFFX-BioB-M_at 364.1 325.9 P
    AFFX-BioB-3_at 368.0 329.9 P
    AFFX-BioC-5_at 263.4 224.2 P
    AFFX-BioC-3_at 371.8 332.8 P
    AFFX-BioDn-5_at 277.0 237.5 P
    View Full Table






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