1 sample(s) found by the keyword GSM143073.


  1. GEO sample ID: GSM143073
    • Sample_geo_accession: GSM143073
    • Sample_status: Public on Jan 20 2007
    • Sample_submission_date: Oct 30 2006
    • Sample_last_update_date: Oct 09 2008
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: 12 degree C-lim anaerobic chemostat culture
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: S. cerevisiae prototrophic haploid reference strain CEN.PK113-7D (MATa)
    • Sample_biomaterial_provider_ch1: Siew Leng Tai
    • Sample_treatment_protocol_ch1: Culture Sample quenched in liquid nitrogen
    • Sample_growth_protocol_ch1: The S. cerevisiae prototrophic haploid reference strain CEN.PK113-7D (MATa) was grown at a dilution rate (D) of 0.03 h-1 at both 12oC in 2-liter chemostats (Applikon, Schiedam, The Netherlands) with a working volume of 1.0 liter as described in {van den Berg, 1996;Tai, 2005}. A temperature probe connected to a cryostat controlled cultures grown at 12oC. Cultures were grown in a defined synthetic medium that was limited by carbon with all other growth requirements in excess as described by {Tai, 2005}. The dilution rate was set at 0.03 hr-1 with pH measured online and kept constant at 5.0 by automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The stirrer speed was set to 600 rpm. Anaerobic growth and steady state conditions were maintained as described {Tai, 2005}. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant at least three volume changes prior to sampling.
    • Sample_growth_protocol_ch1: Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.
    • Sample_growth_protocol_ch1: van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T. & Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953-28959
    • Sample_molecule_ch1: polyA RNA
    • Sample_extract_protocol_ch1: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip┬« microarrays were preformed as described previously in {Piper, 2002}. RNA quality was determined using the Agilent 2100 Bioanalyser. The results for each growth condition were derived from three independently cultured replicates. Data acquisition and analysis as well as statistical analysis were performed as described previously in {Tai, 2005}.
    • Sample_extract_protocol_ch1: Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008.
    • Sample_extract_protocol_ch1: Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.
    • Sample_label_ch1: SAPE
    • Sample_label_protocol_ch1: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip┬« microarrays were preformed as described previously in {Piper, 2002}. RNA quality was determined using the Agilent 2100 Bioanalyser. The results for each growth condition were derived from three independently cultured replicates. Data acquisition and analysis as well as statistical analysis were performed as described previously in {Tai, 2005}.
    • Sample_label_protocol_ch1: Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008.
    • Sample_label_protocol_ch1: Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.
    • Sample_hyb_protocol: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix Genechip┬« microarrays were preformed as described previously in {Piper, 2002}. RNA quality was determined using the Agilent 2100 Bioanalyser. The results for each growth condition were derived from three independently cultured replicates. Data acquisition and analysis as well as statistical analysis were performed as described previously in {Tai, 2005}.
    • Sample_hyb_protocol: Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008.
    • Sample_hyb_protocol: Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M. & Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447.
    • Sample_scan_protocol: Affymetrix scanner 3000
    • Sample_description: S47
    • 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/GSM143nnn/GSM143073/GSM143073.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM143nnn/GSM143073/GSM143073.EXP.gz
    • Sample_series_id: GSE6190
    • 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: 12C anaerobic C-lim chemostat 0.03h-1 (3)
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.7 4.1 A
    AFFX-MurIL10_at 3.3 0.8 A
    AFFX-MurIL4_at 9.6 2.4 A
    AFFX-MurFAS_at 14.4 0.5 A
    AFFX-BioB-5_at 64.2 21.5 P
    AFFX-BioB-M_at 90.3 49.9 P
    AFFX-BioB-3_at 80.4 42.3 P
    AFFX-BioC-5_at 138.8 98.3 P
    AFFX-BioC-3_at 145.8 103.6 P
    AFFX-BioDn-5_at 281.7 237.2 P
    View Full Table






Developed by Dirar Homouz, Gang Chen, and Andrzej S. Kudlicki*

Software download