1 sample(s) found by the keyword GSM200693.


  1. GEO sample ID: GSM200693
    • Sample_geo_accession: GSM200693
    • Sample_status: Public on Oct 16 2007
    • Sample_submission_date: Jun 12 2007
    • Sample_last_update_date: Apr 02 2009
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Chemostat culture
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Strain and Maintenance—This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., and Pronk, J. T. (2000) Enz. Microb. Technol. 26, 706–714]
    • Sample_biomaterial_provider_ch1: L Hazelwood
    • Sample_treatment_protocol_ch1: Liquid nitrogen
    • Sample_growth_protocol_ch1: Chemostat Cultivation—Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953–28959]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0.Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.
    • Sample_growth_protocol_ch1: The synthetic media composition was based on that described by Verduyn (1992). In all chemostats except for those limited by carbon, residual glucose concentration was targeted to 17 g.liter-1 in order to sustain glucose repression at the same level. For anaerobic cultivations, Tween 80 (420 mg.l-1) and ergosterol (10 mg.l-1) were supplemented to the media as described previously to compensate for the inability of S. cerevisiae to synthesise fatty acids in the absence of oxygen. These media contained the following components: for nitrogen-limited cultivation, 0.65 g.liter-1 (NH4)2SO4, 3.0 g.liter-1 KH2PO4, 0.5 g.liter-1 MgSO4•7H2O, 46 g.liter-1 glucose, and 4.5 mg.liter-1 ZnSO4•7H2O.
    • Sample_growth_protocol_ch1: van den Berg, M. A., P. de Jong-Gubbels, C. J. Kortland, J. P. van Dijken, J. T. Pronk, and H. Y. Steensma. 1996. The two acetyl-coenzyme A synthetases of Saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation. J. Biol. Chem. 271:28953-28959.
    • Sample_growth_protocol_ch1: van Dijken, J. P., J. Bauer, L. Brambilla, P. Duboc, J. M. Francois, C. Gancedo, M. L. Giuseppin, J. J. Heijnen, M. Hoare, H. C. Lange, E. A. Madden, P. Niederberger, J. Nielsen, J. L. Parrou, T. Petit, D. Porro, M. Reuss, R. N. van, M. Rizzi, H. Y. Steensma, C. T. Verrips, J. Vindelov, and J. T. Pronk. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb. Technol. 26:706-714.
    • Sample_growth_protocol_ch1: Verduyn, C., E. Postma, W. A. Scheffers, and J. P. van Dijken. 1990. Energetics of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures. J. Gen. Microbiol. 136:405-412.
    • Sample_growth_protocol_ch1: Verduyn, C., E. Postma, W. A. Scheffers, and J. P. van Dijken. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8:501-517.
    • Sample_growth_protocol_ch1: Visser, W., W. A. Scheffers, Batenburg-van der Vegte WH, and J. P. van Dijken. 1990. Oxygen requirements of yeasts. Appl. Environ. Microbiol. 56:3785-3792.
    • Sample_growth_protocol_ch1: Boer, V. M., J. H. de Winde, J. T. Pronk, and M. D. Piper. 2003. The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J. Biol. Chem. 278:3265-3274.
    • Sample_growth_protocol_ch1: Ferea, T. L., D. Botstein, P. O. Brown, and R. F. Rosenzweig. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. U. S. A 96:9721-9726.
    • Sample_growth_protocol_ch1: Jansen, M. L., P. Daran-Lapujade, J. H. de Winde, M. D. Piper, and J. T. Pronk. 2004. Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity. Appl. Environ. Microbiol. 70:1956-1963.
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Microarray analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described in Abbott et al. (2007). Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was g of total RNA. The quality of total RNA, cDNA, cRNA andused, starting with 15 fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies). Results for each growth condition were derived from three independent culture replicates.
    • Sample_extract_protocol_ch1: Abbott DA, Knijnenburg TA, de Poorter LM, Reinders MJ, Pronk JT, van Maris AJ. (2007) Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. doi:10.1111/j.1567-1364.2007.00242.x
    • Sample_label_ch1: biotin
    • Sample_label_protocol_ch1: EukGE-ws2v4
    • Sample_label_protocol_ch1: Microarray analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described in Abbott et al. (2007). Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target g of total RNA. The quality of totallabelling assay was used, starting with 15 RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies). Results for each growth condition were derived from three independent culture replicates.
    • Sample_label_protocol_ch1: Abbott DA, Knijnenburg TA, de Poorter LM, Reinders MJ, Pronk JT, van Maris AJ. (2007) Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. doi:10.1111/j.1567-1364.2007.00242.x
    • Sample_hyb_protocol: Microarray analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described in Abbott et al. (2007). Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was g of total RNA. The quality of total RNA, cDNA, cRNA andused, starting with 15 fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies). Results for each growth condition were derived from three independent culture replicates.
    • Sample_hyb_protocol: Abbott DA, Knijnenburg TA, de Poorter LM, Reinders MJ, Pronk JT, van Maris AJ. (2007) Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. doi:10.1111/j.1567-1364.2007.00242.x
    • Sample_scan_protocol: Affymetrix scanner 3000
    • Sample_description: LH23
    • Sample_data_processing: GCOS
    • 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/GSM200nnn/GSM200693/GSM200693.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM200nnn/GSM200693/GSM200693.CHP.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM200nnn/GSM200693/GSM200693.EXP.gz
    • Sample_series_id: GSE8089
    • Sample_series_id: GSE11452
    • Sample_series_id: GSE15465
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Carbon-limited anaerobic chemostat with benzoate -1
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 1.08891 2.3031 A
    AFFX-MurIL10_at 2.68924 1.59145 A
    AFFX-MurIL4_at 6.36277 1.23479 A
    AFFX-MurFAS_at 8.45316 1.21679 A
    AFFX-BioB-5_at 119.57 53.3604 P
    AFFX-BioB-M_at 161.929 97.8118 P
    AFFX-BioB-3_at 131.335 73.311 P
    AFFX-BioC-5_at 197.012 135.574 P
    AFFX-BioC-3_at 265.038 201.828 P
    AFFX-BioDn-5_at 476.627 411.234 P
    View Full Table






Developed by Dirar Homouz, Gang Chen, and Andrzej S. Kudlicki*

Software download