1 sample(s) found by the keyword GSM387540.


  1. GEO sample ID: GSM387540
    • Sample_geo_accession: GSM387540
    • Sample_status: Public on Aug 20 2009
    • Sample_submission_date: Mar 30 2009
    • Sample_last_update_date: Aug 20 2009
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: C-lim anaerobic chemostat of msn2msn4 double mutant
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: genotype: cen.pk113-7d prototropic strain mata mal2-8c suc2 ura3 msn2: :loxP msn4::loxP-kanMX-loxP p426(URA3)
    • Sample_biomaterial_provider_ch1: L. Hazelwood
    • Sample_treatment_protocol_ch1: Quenching in liquid nitrogen
    • Sample_growth_protocol_ch1: Media for chemostat cultivation. The synthetic medium composition was based on that described by Verduyn (1). The modifications introduced for carbon, nitrogen, sulphur, phosphorus and zinc limited growth were determined previously (1-3) and are listed in Table 2. In all chemostats except for those limited by carbon, the residual glucose concentration was targeted to 17 g/l (95 mM) in order to have the same degree of glucose repression. The reservoir medium was supplemented with vitamins and the anaerobic growth factors Tween-80 and ergosterol as previously described (1).
    • Sample_growth_protocol_ch1: Chemostat cultivation. Chemostat cultures were fed with synthetic medium that limited growth by carbon, nitrogen, sulphur, phosphorus or zinc with all other growth requirements in excess and at constant residual concentration. The dilution rate was set at 0.10 h-1, the pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH as previously described (3). Cultures were assumed to be in steady-state when, after at least 5 volume changes, culture dry-weight, glucose concentration, carbon-dioxide production rate and oxygen consumption rate varied by less than 2 % during one additional volume change (4). Steady-state samples were taken after 10 generations at the latest to avoid strain adaptation due to long-term cultivation (5). Each cultivation condition was performed in triplicate.
    • Sample_growth_protocol_ch1: Reference List
    • Sample_growth_protocol_ch1: 1.Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) J. Gen. Microbiol. 136, 405-412
    • Sample_growth_protocol_ch1: 2.De Nicola, R., Hazelwood, L. A., De Hulster, E. A., Walsh, M. C., Knijnenburg, T. A., Reinders, M. J., Walker, G. M., Pronk, J. T., Daran, J. M., and Daran-Lapujade, P. (2007) Appl. Environ. Microbiol. 73, 7680-7692
    • Sample_growth_protocol_ch1: 3.Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M., and Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447
    • Sample_growth_protocol_ch1: 4.Ferea, T. L., Botstein, D., Brown, P. O., and Rosenzweig, R. F. (1999) Proc. Natl. Acad. Sci. U. S. A 96, 9721-9726
    • Sample_growth_protocol_ch1: 5.Jansen, M. L., Daran-Lapujade, P., de Winde, J. H., Piper, M. D., and Pronk, J. T. (2004) Appl. Environ. Microbiol. 70, 1956-1963
    • Sample_growth_protocol_ch1: 6.Boer, V. M., de Winde, J. H., Pronk, J. T., and Piper, M. D. (2003) J. Biol. Chem. 278, 3265-3274
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Microarrays, data acquisition and statistical analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described (2). Results for each growth condition were derived from three independent culture replicates. Acquisition and quantification of array images and data filtering were performed using Affymetrix GeneChipĀ® Operating Software version 1.2. To eliminate insignificant variations, genes with expression values below 12 were set to 12 as previously described (6).
    • Sample_extract_protocol_ch1: Reference List
    • Sample_extract_protocol_ch1: 1. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) J. Gen. Microbiol. 136, 405-412
    • Sample_extract_protocol_ch1: 2. De Nicola, R., Hazelwood, L. A., De Hulster, E. A., Walsh, M. C., Knijnenburg, T. A., Reinders, M. J., Walker, G. M., Pronk, J. T., Daran, J. M., and Daran-Lapujade, P. (2007) Appl. Environ. Microbiol. 73, 7680-7692
    • Sample_extract_protocol_ch1: 3. Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M., and Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447
    • Sample_extract_protocol_ch1: 4. Ferea, T. L., Botstein, D., Brown, P. O., and Rosenzweig, R. F. (1999) Proc. Natl. Acad. Sci. U. S. A 96, 9721-9726
    • Sample_extract_protocol_ch1: 5. Jansen, M. L., Daran-Lapujade, P., de Winde, J. H., Piper, M. D., and Pronk, J. T. (2004) Appl. Environ. Microbiol. 70, 1956-1963
    • Sample_extract_protocol_ch1: 6. Boer, V. M., de Winde, J. H., Pronk, J. T., and Piper, M. D. (2003) J. Biol. Chem. 278, 3265-3274
    • Sample_label_ch1: biotin
    • Sample_label_protocol_ch1: Microarrays, data acquisition and statistical analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described (2). Results for each growth condition were derived from three independent culture replicates. Acquisition and quantification of array images and data filtering were performed using Affymetrix GeneChipĀ® Operating Software version 1.2. To eliminate insignificant variations, genes with expression values below 12 were set to 12 as previously described (6).
    • Sample_label_protocol_ch1: Reference List
    • Sample_label_protocol_ch1: 1. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) J. Gen. Microbiol. 136, 405-412
    • Sample_label_protocol_ch1: 2. De Nicola, R., Hazelwood, L. A., De Hulster, E. A., Walsh, M. C., Knijnenburg, T. A., Reinders, M. J., Walker, G. M., Pronk, J. T., Daran, J. M., and Daran-Lapujade, P. (2007) Appl. Environ. Microbiol. 73, 7680-7692
    • Sample_label_protocol_ch1: 3. Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M., and Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447
    • Sample_label_protocol_ch1: 4. Ferea, T. L., Botstein, D., Brown, P. O., and Rosenzweig, R. F. (1999) Proc. Natl. Acad. Sci. U. S. A 96, 9721-9726
    • Sample_label_protocol_ch1: 5. Jansen, M. L., Daran-Lapujade, P., de Winde, J. H., Piper, M. D., and Pronk, J. T. (2004) Appl. Environ. Microbiol. 70, 1956-1963
    • Sample_label_protocol_ch1: 6. Boer, V. M., de Winde, J. H., Pronk, J. T., and Piper, M. D. (2003) J. Biol. Chem. 278, 3265-3274
    • Sample_hyb_protocol: According to manufacturer's procedures
    • Sample_scan_protocol: Data acquisition was performed using the Affymetrix scanner 3000, quantification of array images and data filtering were performed with the Affymetrix software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0.
    • Sample_description: C-lim, ANAE
    • Sample_description: LH56
    • Sample_data_processing: GCOS
    • 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/GSM387nnn/GSM387540/GSM387540.CEL.gz
    • Sample_series_id: GSE15465
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: C-lim anaerobic chemostat of msn2msn4 double mutant -3
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.2 0.9 A
    AFFX-MurIL10_at 0.7 0.3 A
    AFFX-MurIL4_at 3.1 0.5 A
    AFFX-MurFAS_at 5.6 1.5 A
    AFFX-BioB-5_at 86.4 44.7 P
    AFFX-BioB-M_at 117.1 78.6 P
    AFFX-BioB-3_at 104.8 68.2 P
    AFFX-BioC-5_at 151.2 113.8 P
    AFFX-BioC-3_at 176.4 137.3 P
    AFFX-BioDn-5_at 271.6 231.3 P
    View Full Table






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