1 sample(s) found by the keyword GSM225467.


  1. GEO sample ID: GSM225467
    • Sample_geo_accession: GSM225467
    • 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: Prologued aerobic glucose limited chemostat culture 200 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. Kötter, Frankfurt, Germany
    • Sample_biomaterial_provider_ch1: MLA Jansen
    • Sample_treatment_protocol_ch1: Liquid nitrogen quenching
    • Sample_growth_protocol_ch1: Media.
    • Sample_growth_protocol_ch1: Synthetic medium containing mineral salts and vitamins was prepared and sterilized as described by Verduyn et al. (1992). For chemostat cultivation, the glucose concentration in reservoir media was 7·5 g l–1 (0·25 mol C l–1). This medium composition has previously been demonstrated to sustain glucose-limited cultivation of S. cerevisiae CEN.PK113-7D (Lange & Heijnen, 2001; Verduyn et al., 1992). For batch cultivation, the initial glucose concentration was 20 g l–1.
    • Sample_growth_protocol_ch1: Chemostat cultivation.
    • Sample_growth_protocol_ch1: Aerobic chemostat cultivation was performed at a dilution rate of 0·10 h–1 at 30 °C in 1·5 l laboratory fermenters (Applikon) at a stirrer speed of 800 r.p.m. The working volume of the cultures was kept at 1·0 l by a peristaltic effluent pump coupled to an electrical level sensor. This set-up ensured that under all growth conditions, biomass concentrations in samples taken directly from the culture differed by <1 % from those 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 (Applikon), via the automatic addition of 2 mol KOH l–1. The fermenter was flushed with air at a flow rate of 0·5 l min–1 using a Brooks 5876 mass-flow controller. The dissolved-oxygen concentration was continuously monitored with an oxygen electrode (model 34 100 3002; Ingold), and it remained above 60 % of air saturation. Chemostat cultures were routinely checked for potential bacterial and fungal infection by phase-contrast microscopy.
    • Sample_growth_protocol_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_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Cells were rapidly (within 3 s) transferred from the chemostat culture into liquid nitrogen to immediately quench the metabolism. The frozen cell suspension (about 40 g cell broth) was thawed gently on ice. After complete thawing, the cell suspension was centrifuged at 0 °C, 5000 g, for 5 min. Total RNA extraction from the pellets was performed using the hot-phenol 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: P41
    • 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/GSM225467/GSM225467.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM225nnn/GSM225467/GSM225467.EXP.gz
    • Sample_series_id: GSE8898
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Prolongued aerobic glucose limited chemostat culture D=0.1/h -3
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.0 0.5 A
    AFFX-MurIL10_at 0.1 0.3 A
    AFFX-MurIL4_at 0.2 0.3 A
    AFFX-MurFAS_at 0.6 0.9 A
    AFFX-BioB-5_at 103.7 63.2 P
    AFFX-BioB-M_at 139.4 100.8 P
    AFFX-BioB-3_at 105.9 68.8 P
    AFFX-BioC-5_at 158.4 118.8 P
    AFFX-BioC-3_at 150.6 111.9 P
    AFFX-BioDn-5_at 157.1 118.6 P
    View Full Table






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