1 sample(s) found by the keyword GSM225469.


  1. GEO sample ID: GSM225469
    • Sample_geo_accession: GSM225469
    • Sample_status: Public on Aug 31 2007
    • Sample_submission_date: Aug 29 2007
    • Sample_last_update_date: Oct 09 2008
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Steady state Anaerobic glucose limited chemostat culture with 100%CO2
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: The prototrophic S. cerevisiae strain CEN.PK113-7D was used for this study
    • Sample_biomaterial_provider_ch1: J Aguilera
    • Sample_treatment_protocol_ch1: Liquid nitrogen quenching
    • Sample_growth_protocol_ch1: 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.
    • Sample_growth_protocol_ch1: Synthetic media were prepared as described [20] 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.
    • Sample_growth_protocol_ch1: For CO2-enriched anaerobic cultivation, the nitrogen sparging gas was replaced by pure (>99.99%) CO2 (HoekLoos, Schiedam, The Netherlands).
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: 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).
    • Sample_label_ch1: Biotinylated dUTP - streptavidine Phycoerythrin (SAPE)
    • Sample_label_protocol_ch1: 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).
    • Sample_hyb_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).
    • Sample_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).
    • Sample_description: J02
    • 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/GSM225469/GSM225469.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM225nnn/GSM225469/GSM225469.EXP.gz
    • Sample_series_id: GSE8900
    • Sample_series_id: GSE11452
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Anaerobic glucose limited chemostat culture with 100% CO2 D=0.1/h -2
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.4 0.9 A
    AFFX-MurIL10_at 2.1 0.3 A
    AFFX-MurIL4_at 5.4 0.2 A
    AFFX-MurFAS_at 8.7 0.5 A
    AFFX-BioB-5_at 115.9 73.0 P
    AFFX-BioB-M_at 157.3 120.6 P
    AFFX-BioB-3_at 152.9 117.6 P
    AFFX-BioC-5_at 198.2 160.3 P
    AFFX-BioC-3_at 156.0 120.1 P
    AFFX-BioDn-5_at 191.5 153.5 P
    View Full Table






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