1 sample(s) found by the keyword GSM225577.


  1. GEO sample ID: GSM225577
    • Sample_geo_accession: GSM225577
    • Sample_status: Public on Jun 20 2008
    • Sample_submission_date: Aug 29 2007
    • Sample_last_update_date: Jun 20 2008
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Steady state Aerobic formaldehyde-glucose limited chemostat culture (separate feeding)
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: The haploid, prototrophic S. cerevisiae strain CEN.PK113-7D (MATa MAL2-8c SUC2) was obtained from Dr P. Kotter, Frankfurt, Germany.
    • Sample_biomaterial_provider_ch1: Erik de Hulster
    • Sample_treatment_protocol_ch1: Liquid nitrogen quenching
    • Sample_growth_protocol_ch1: Aerobic chemostat cultivation was performed at 30ºC in 1.5 L laboratory fermenters (Applikon, Schiedam, the Netherlands) with a stirrer speed of 800 rpm. The working volume was kept at 1 L by a Masterflex peristaltic effluent pump (Barrington IL, USA) coupled to an electric level sensor. The pH was kept at 5.0 using an Applikon ADI 1030 biocontroller via automatic addition of 2.0 M potassium hydroxide. Cultures were sparged with air at a flow rate of 0.5 L.min-1 using Brooks 5876 mass-flow controllers. The dissolved oxygen tension (DOT) was continuously monitored with an oxygen electrode (Ingold, model 34.100.3002, Mettler, Utrecht, the Netherlands) and remained above 50% of air saturation in all chemostat cultures. The dilution rate (in steady-state cultures equal to the specific growth rate) was set to 0.10 h-1.
    • Sample_growth_protocol_ch1: Synthetic medium was prepared as described previously (Verduyn et al., 1992) with glucose (7.5 g.L 1) as the sole carbon source. Filter sterilized vitamins were either added directly to the medium or were added from a separate reservoir. Formaldehyde was prepared by hydrolysing para-formaldehyde in 15 mM ammonium hydroxide (30 min. incubation at 100ºC) and aseptically added to the medium reservoir at various concentrations as indicated in the results section. When formaldehyde was co-fed, S. cerevisiae was first cultivated in batch on glucose alone, followed by 3-days with 30 mM formaldehyde in the medium vessel after which the medium was switched to the final amount of formaldehyde until a steady state was obtained. Steady state was defined as the situation in which at least five volume changes had passed since the last change in culture parameters, and in which the biomass concentration, as well as all other specific production or consumption rates, had remained constant (<2% variation) for at least two volume changes.
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Sampling of the chemostat grown cells from aerobic glucose-limited chemostats with or with-out co-feeding of formaldehyde, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Knijnenburg et al 2007).
    • Sample_extract_protocol_ch1: Knijnenburg TA, de Winde JH, Daran JM, Daran-Lapujade P, Pronk JT, Reinders MJ, Wessels LF (2007) Exploiting combinatorial cultivation conditions to infer transcriptional regulation.
    • Sample_extract_protocol_ch1: BMC Genomics. 8:25.
    • Sample_label_ch1: Biotinylated dUTP - streptavidine Phycoerythrin (SAPE)
    • Sample_label_protocol_ch1: Sampling of the chemostat grown cells from aerobic glucose-limited chemostats with or with-out co-feeding of formaldehyde, probe preparation, and hybridization to Affymetrix Genechip® microarrays were
    • Sample_label_protocol_ch1: performed as described previously (Knijnenburg et al 2007).
    • Sample_label_protocol_ch1: Knijnenburg TA, de Winde JH, Daran JM, Daran-Lapujade P, Pronk JT, Reinders MJ, Wessels LF (2007) Exploiting combinatorial cultivation conditions to infer transcriptional regulation.
    • Sample_label_protocol_ch1: BMC Genomics. 8:25.
    • Sample_hyb_protocol: Sampling of the chemostat grown cells from aerobic glucose-limited chemostats with or with-out co-feeding of formaldehyde, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Knijnenburg et al 2007).
    • Sample_hyb_protocol: Knijnenburg TA, de Winde JH, Daran JM, Daran-Lapujade P, Pronk JT, Reinders MJ, Wessels LF (2007) Exploiting combinatorial cultivation conditions to infer transcriptional regulation.
    • Sample_hyb_protocol: BMC Genomics. 8:25.
    • Sample_scan_protocol: Sampling of the chemostat grown cells from aerobic glucose-limited chemostats with or with-out co-feeding of formaldehyde, probe preparation, and hybridization to Affymetrix Genechip® microarrays were performed as described previously (Knijnenburg et al 2007).
    • Sample_scan_protocol: Knijnenburg TA, de Winde JH, Daran JM, Daran-Lapujade P, Pronk JT, Reinders MJ, Wessels LF (2007) Exploiting combinatorial cultivation conditions to infer transcriptional regulation.
    • Sample_scan_protocol: BMC Genomics. 8:25.
    • Sample_description: ES66
    • Sample_data_processing: GCOS version 2.1 calculated intensity data with global scaling to 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/GSM225577/GSM225577.CEL.gz
    • Sample_series_id: GSE8902
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Aerobic formaldehyde-glucose limited chemostat culture D=0.1/h -2 (separate feeding)
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.1 0.3 A
    AFFX-MurIL10_at 0.1 0.3 A
    AFFX-MurIL4_at 0.5 0.6 A
    AFFX-MurFAS_at 2.2 1.6 A
    AFFX-BioB-5_at 75.4 29.9 P
    AFFX-BioB-M_at 102.9 58.2 P
    AFFX-BioB-3_at 81.2 39.1 P
    AFFX-BioC-5_at 125.3 80.6 P
    AFFX-BioC-3_at 141.5 97 P
    AFFX-BioDn-5_at 309.9 266.3 P
    View Full Table






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