1 sample(s) found by the keyword GSM453348.


  1. GEO sample ID: GSM453348
    • Sample_geo_accession: GSM453348
    • Sample_status: Public on Sep 25 2009
    • Sample_submission_date: Sep 16 2009
    • Sample_last_update_date: Sep 24 2009
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Chemostat culture
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: strain: gg3201
    • Sample_characteristics_ch1: genotype: mata mal2-8c suc2 snf7: :loxP-kanr-loxP
    • Sample_biomaterial_provider_ch1: JM Daran
    • Sample_treatment_protocol_ch1: liquid N2 quenching
    • Sample_growth_protocol_ch1: Anaerobic glucose-limited chemostat cultures were grown at a dilution rate of 0.10 h-1 on a synthetic medium supplemented with the anaerobic growth factors Tween-80 and ergosterol as described previously (Tai et al., 2005). Independent triplicate fermentations were run for the snf7Δ strain and the reference strain CEN.PK113-7D. In brief, 2-l Applikon fermenters with a working volume of 1 l were used at a temperature of 30oC and a stirrer speed of 800 rpm. Culture pH was kept at 5.0 by the automatic addition of 2 M KOH. Oxygen and carbon dioxide concentrations in the off-gas were measured with a NGA 2000 Rosemount gas analyser. Substrate and metabolite concentrations in culture supernatants and media were analysed by high performance liquid chromatography on an Aminex HPX-87H column (Biorad, Hercules, CA) with 5 mM H2SO4 as the mobile phase. Culture dry weights were determined via filtration (Postma et al., 1989).
    • Sample_growth_protocol_ch1: Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran JM & Pronk JT (2005) Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J Biol Chem 280: 437-447.
    • Sample_growth_protocol_ch1: Postma E, Verduyn C, Scheffers WA & van Dijken JP (1989) Enzymic analysis of the crabtree effect in glucose-limited chemostat cultures of Saccharomyces cerevisiae. Appl Environ Microbiol 55: 468-477.
    • Sample_molecule_ch1: polyA RNA
    • Sample_extract_protocol_ch1: For the culture of GG3201 (snf7delta) and its isogenic reference CEN.PK113-7D the rapid broth quenching in liquid nitrogen, RNA isolation and transcriptome analysis with Affymetrix microarrays were performed as described previously (Daran-Lapujade et al., 2004)
    • Sample_extract_protocol_ch1: Daran-Lapujade P, Jansen ML, Daran JM, van Gulik W, de Winde JH & Pronk JT (2004) Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J Biol Chem 279: 9125-9138.
    • Sample_label_ch1: biotin
    • Sample_label_protocol_ch1: For the culture of GG3201 (snf7delta) and its isogenic reference CEN.PK113-7D the rapid broth quenching in liquid nitrogen, RNA isolation and transcriptome analysis with Affymetrix microarrays were performed as described previously (Daran-Lapujade et al., 2004)
    • Sample_label_protocol_ch1: Daran-Lapujade P, Jansen ML, Daran JM, van Gulik W, de Winde JH & Pronk JT (2004) Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J Biol Chem 279: 9125-9138.
    • Sample_hyb_protocol: For the culture of GG3201 (snf7delta) and its isogenic reference CEN.PK113-7D the rapid broth quenching in liquid nitrogen, RNA isolation and transcriptome analysis with Affymetrix microarrays were performed as described previously (Daran-Lapujade et al., 2004)
    • Sample_hyb_protocol: Daran-Lapujade P, Jansen ML, Daran JM, van Gulik W, de Winde JH & Pronk JT (2004) Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J Biol Chem 279: 9125-9138.
    • Sample_scan_protocol: For the culture of GG3201 (snf7delta) and its isogenic reference CEN.PK113-7D the rapid broth quenching in liquid nitrogen, RNA isolation and transcriptome analysis with Affymetrix microarrays were performed as described previously (Daran-Lapujade et al., 2004)
    • Sample_scan_protocol: Daran-Lapujade P, Jansen ML, Daran JM, van Gulik W, de Winde JH & Pronk JT (2004) Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J Biol Chem 279: 9125-9138.
    • Sample_description: S45
    • Sample_data_processing: MAS 5.0 CHP 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/GSM453nnn/GSM453348/GSM453348.CEL.gz
    • Sample_series_id: GSE18128
    • 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 with the rim101 delta mutant-1
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.0 0.8 A
    AFFX-MurIL10_at 0.1 0.2 A
    AFFX-MurIL4_at 1.0 0.3 A
    AFFX-MurFAS_at 4.1 0.4 A
    AFFX-BioB-5_at 83.6 40.2 P
    AFFX-BioB-M_at 80.2 39.0 P
    AFFX-BioB-3_at 78.0 38.7 P
    AFFX-BioC-5_at 134.8 95.5 P
    AFFX-BioC-3_at 144.5 105.0 P
    AFFX-BioDn-5_at 233.7 197.5 P
    View Full Table






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