1 sample(s) found by the keyword GSM234644.


  1. GEO sample ID: GSM234644
    • Sample_geo_accession: GSM234644
    • Sample_status: Public on Oct 17 2007
    • Sample_submission_date: Oct 04 2007
    • Sample_last_update_date: Oct 09 2008
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Chemostat sample
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Saccharomyces cerevisiae CENPK113-7D (MATa)
    • Sample_biomaterial_provider_ch1: M. Almering
    • Sample_treatment_protocol_ch1: N2 quenching
    • Sample_growth_protocol_ch1: The laboratory reference strain CEN.PK 113-7D (MATa) was grown at 30 °C in 2-L chemostat fermentors (Applikon, Schiedam, The Netherlands) with a working volume of 1-L using an electronic level sensor to maintain a constant volume. All cultures, including the reference, were fed with minimal medium as described by Verduyn et al. (1992) with 25 g L-1 glucose as the limiting nutrient and 0.15 ml L-1 silicone antifoam (BDH, Poole, England) to prevent excessive foaming. The dilution rate was set to 0.10 h-1 and the pH was controlled at 5.0 with the automatic addition (ADI 1031 bio controller, Applikon) of 2 M KOH. The stirrer speed was set at 800 RPM and anaerobicity was maintained by sparging the fermentor with N2 gas at 500 ml min-1. To prevent diffusion of oxygen, the fermentor was equipped with Norprene tubing and Viton O-rings and the medium vessel was also flushed with N2 gas. A comparable degree of weak acid uncoupling was ensured by decreasing the biomass yield to approximately 50% of the reference condition (no organic acids added) with the addition of the appropriate concentration of acetic acid, sodium benzoate, propionic acid or potassium sorbate to the reservoir media.
    • Sample_growth_protocol_ch1: Verduyn C, Postma E, Scheffers WA & van Dijken JP (1992) Effect of benzoic acid on metabolic fluxes in yeast: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-517.
    • Sample_molecule_ch1: polyA RNA
    • Sample_extract_protocol_ch1: Samples from the chemostat cultures were taken as rapidly as possible to limit any potential changes in transcript profiles during the procedure. 40–60 ml of culture broth was sampled directly from the chemostat into a beaker containing 200 ml of liquid nitrogen. With vigorous stirring, the sample froze instantly. The frozen sample was then broken into small fragments and transferred to a 50-ml centrifuge tube. The sample was then thawed at room temperature, ensuring that it remained as close to zero as possible. Cells were pelleted (5000 rpm at 0 °C for 4 min), resuspended in 2 ml of ice-cold AE buffer (50 mM sodium acetate, 10 mM EDTA, pH 5.0) and aliquoted into 5 Eppendorf tubes. This corresponded to _20 mg of dry weight per tube. For each array, total RNA was extracted from a single tube using the hot-phenol method (32) or the FastRNA kit, Red (BIO 101, Inc., Vista, CA).
    • Sample_label_ch1: Biotinylated-UTP SAPE-Phycoerythrin
    • Sample_label_protocol_ch1: mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.
    • Sample_label_protocol_ch1: (1) Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual, Santa Clara, CA
    • Sample_hyb_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.
    • Sample_hyb_protocol: (1) Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual, Santa Clara, CA
    • Sample_scan_protocol: scanning with the Affymetrix GeneArray Scanner.
    • Sample_description: MA76
    • Sample_data_processing: Acquisition and quantification of array images as well as primary data analysis were performed using the Affymetrix software packages: Microarray Suite version 4.0.1, MicroDB version 2.0, and Data Mining Tool version 2.0. Microsoft Excel was used for further statistical analyses. All arrays were globally scaled to a target value of 150 using the average signal from all gene features using Microarray Suite version 4.0.1. When pairwise comparisons were performed (using Microarray Suite version 4.0.1), a transcript was considered “changed” when a call of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.
    • 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/GSM234nnn/GSM234644/GSM234644.CEL.gz
    • Sample_series_id: GSE9232
    • 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: Carbon-limited anaerobic chemostat with benzoate -3
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 1.1 6.0 A
    AFFX-MurIL10_at 2.3 3.0 A
    AFFX-MurIL4_at 6.6 6.7 A
    AFFX-MurFAS_at 8.4 4.9 A
    AFFX-BioB-5_at 104.5 63.1 A
    AFFX-BioB-M_at 106.5 69.3 P
    AFFX-BioB-3_at 95.1 59.9 P
    AFFX-BioC-5_at 188.0 151.2 P
    AFFX-BioC-3_at 124.6 88.3 P
    AFFX-BioDn-5_at 114.8 77.3 P
    View Full Table






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