1 sample(s) found by the keyword GSM87661.


  1. GEO sample ID: GSM87661
    • Sample_geo_accession: GSM87661
    • Sample_status: Public on Dec 16 2005
    • Sample_submission_date: Dec 14 2005
    • Sample_last_update_date: Dec 15 2005
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: glucose pulse perturbation to a chemostat culture (initial steady state)
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Strain CEN.PK113-7D Mata prototroph
    • Sample_biomaterial_provider_ch1: Penia Kresnowati
    • Sample_treatment_protocol_ch1: Liquid nitrogen quenching
    • Sample_treatment_protocol_ch1: Sampling for Microarrays - Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.
    • Sample_treatment_protocol_ch1: Piper,M.D., Daran-Lapujade,P., Bro,C., Regenberg,B., Knudsen,S., Nielsen,J., and 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_growth_protocol_ch1: Chemostat cultivation – Saccharomyces cerevisiae (CEN PK 113-7D) was cultivated in an aerobic carbon-limited chemostat culture in a 7-litres fermentor (Applikon, The Netherlands) with a working volume of 4-l on the adapted doubled mineral medium (Verduyn et al., 1992) with 27.1 g.l-1 of glucose and 1.42 g.l-1 of ethanol, to support a biomass concentration of about 15 g dry weight.l-1. The dilution rate was set to be 0.05 hr-1 and the airflow rate was set to be 200 l.hr-1. Other fermentation parameters are: a pH controlled at 5, a temperature controlled at 30˚C, an overpressure of 0.3 bar and stirrer speed of 600 rpm. The chemostat was considered to obtain its stable steady state condition 5 resident times after the end of its batch phase.
    • Sample_growth_protocol_ch1: Glucose pulse experiment - At the age of 7 dilution times, the steady state chemostat culture was perturbed by the addition of 20 ml of glucose solution (200 g/l) to the fermentor so that the residual glucose concentration was suddenly increased to about 1 g/l (5.56 mM). The glucose solution was rapidly injected by a pneumatic system (< 1 s). Samples were taken prior to the glucose pulse (steady state samples) and within 360 s transient after the perturbation.
    • Sample_growth_protocol_ch1:
    • Sample_growth_protocol_ch1:
    • Sample_growth_protocol_ch1: Reference List
    • Sample_growth_protocol_ch1:
    • Sample_growth_protocol_ch1: Verduyn,C., Postma,E., Scheffers,W.A., and van Dijken,J.P. (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:
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Total RNA extracted as described by Piper et al (2002)
    • Sample_extract_protocol_ch1: Piper,M.D., Daran-Lapujade,P., Bro,C., Regenberg,B., Knudsen,S., Nielsen,J., and 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_ch1: Biotynilated cRNA
    • Sample_label_protocol_ch1: probe preparation were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.
    • Sample_label_protocol_ch1: Piper,M.D., Daran-Lapujade,P., Bro,C., Regenberg,B., Knudsen,S., Nielsen,J., and 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: Hybridization to Affymetrix Genechip® microarrays were performed as described previously (Piper et al., 2002) The results for each time point (initial stead state, 30, 60, 120, 300 and 330) were derived from at least two independently cultured replicates. The time point at 210 seconds was derived from a single culture.
    • Sample_hyb_protocol: Piper,M.D., Daran-Lapujade,P., Bro,C., Regenberg,B., Knudsen,S., Nielsen,J., and 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: Array scan twice
    • Sample_scan_protocol: pixel value 3micron
    • Sample_scan_protocol: Wl 570 mn
    • Sample_scan_protocol: affymetrix scanner 3000
    • Sample_description: Replicate arrays MA56 and MA64
    • Sample_data_processing: Data processed with Affymetrix GCOS software
    • 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/GSM87nnn/GSM87661/GSM87661.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM87nnn/GSM87661/GSM87661.EXP.gz
    • Sample_series_id: GSE3821
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: MA78 glucose pulse 1 T=120 seconds
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.2 0.7 A
    AFFX-MurIL10_at 0.3 0.4 A
    AFFX-MurIL4_at 0.8 0.4 A
    AFFX-MurFAS_at 1.8 0.5 A
    AFFX-BioB-5_at 87.6 55.2 P
    AFFX-BioB-M_at 108.6 78.7 P
    AFFX-BioB-3_at 104.5 75.6 P
    AFFX-BioC-5_at 160.1 130.5 P
    AFFX-BioC-3_at 136.3 108.1 P
    AFFX-BioDn-5_at 150.1 122.8 P
    View Full Table






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