1 sample(s) found by the keyword GSM209973.


  1. GEO sample ID: GSM209973
    • Sample_geo_accession: GSM209973
    • Sample_status: Public on Jun 01 2008
    • Sample_submission_date: Jul 12 2007
    • Sample_last_update_date: Aug 08 2007
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: carbon limited chemostat 0.1h-1
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Saccharomyces cerevisiae CEN.PK 113-7D (MATa, SUC2, MAL2-8 c)
    • Sample_biomaterial_provider_ch1: R. Verwall
    • Sample_treatment_protocol_ch1: fermentation sample quenched in liquid nitrogen
    • Sample_growth_protocol_ch1: Chemostat cultivation
    • Sample_growth_protocol_ch1: Strains CEN.PK113-7D was grown at 30°C in 2 liter (L) chemostats (Applikon) with a working volume of 1.0 L. Cultures were fed with a defined mineral medium that limited growth by glucose (C-limited) with all other growth requirements in excess and at a constant residual concentration. Strains CEN.PK113-7D was grown on synthetic medium containing 7,5 g L-1 glucose to maintain carbon limitation. The dilution rate was set at 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 bio controller. Stirrer speed was 800 rpm, and the airflow was 0.5 L min-1. Dissolved oxygen tension was measured on line with an Ingold model 34-100-3002 probe and was above 50% of air saturation. The off-gas was cooled by a condenser connected to a cryostat set at 2°C, and oxygen and carbon dioxide were measured off-line with an NGA 2000 Rosemount gas analyzer. Steady-state samples were taken after ~10-14 volume changes to avoid strain adaptation due to long term cultivation. Dry weight, glucose and ethanol levels, dissolved oxygen and gas profiles had to be constant over at least 3 volume changes before sampling for RNA extraction.
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Sampling of CEN.PK113-7D from aerobic C-limited chemostats with glucose as sole carbon source, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously by Piper et al. (2002). The results for each growth condition were derived from three or more independently cultured replicates.
    • Sample_extract_protocol_ch1: Piper, M. D., P. Daran-Lapujade, C. Bro, B. Regenberg, S. Knudsen, J. Nielsen, and J. T. Pronk. 2002. Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem. 277:37001-8.
    • Sample_label_ch1: SAPE (Phycoerythrin)
    • Sample_label_protocol_ch1: Sampling of CEN.PK113-7D from aerobic C-limited chemostats with glucose as sole carbon source, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously by Piper et al. (2002). The results for each growth condition were derived from three or more independently cultured replicates.
    • Sample_label_protocol_ch1: Piper, M. D., P. Daran-Lapujade, C. Bro, B. Regenberg, S. Knudsen, J. Nielsen, and J. T. Pronk. 2002. Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem. 277:37001-8.
    • Sample_hyb_protocol: Sampling of CEN.PK113-7D from aerobic C-limited chemostats with glucose as sole carbon source, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously by Piper et al. (2002). The results for each growth condition were derived from three or more independently cultured replicates.
    • Sample_hyb_protocol: Piper, M. D., P. Daran-Lapujade, C. Bro, B. Regenberg, S. Knudsen, J. Nielsen, and J. T. Pronk. 2002. Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem. 277:37001-8.
    • Sample_scan_protocol: Affymetrix scanner 3000
    • Sample_description: MA54
    • Sample_data_processing: Affymetrix GCOS version 2.1 CHIP file targetted 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/GSM209nnn/GSM209973/GSM209973.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM209nnn/GSM209973/GSM209973.EXP.gz
    • Sample_series_id: GSE8451
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: CENPK113-7D glucose limited chemostat
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.3 1.0 A
    AFFX-MurIL10_at 0.4 0.7 A
    AFFX-MurIL4_at 1.1 0.2 A
    AFFX-MurFAS_at 4.1 3.2 A
    AFFX-BioB-5_at 91.9 49.5 P
    AFFX-BioB-M_at 107.7 67.1 P
    AFFX-BioB-3_at 90.7 54.4 P
    AFFX-BioC-5_at 158.9 120.3 P
    AFFX-BioC-3_at 149.9 110.2 P
    AFFX-BioDn-5_at 152.7 114.5 P
    View Full Table






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