1 sample(s) found by the keyword GSM209979.


  1. GEO sample ID: GSM209979
    • Sample_geo_accession: GSM209979
    • Sample_status: Public on Jun 01 2008
    • Sample_submission_date: Jul 12 2007
    • Sample_last_update_date: Oct 09 2008
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: carbon limited chemostat 0.1h-1
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Saccharomyces cerevisiae CEN.PK 113-7D (MATa, SUC2, MAL2-8 c)
    • Sample_biomaterial_provider_ch1: R. Verwall
    • Sample_treatment_protocol_ch1: fermentation sample quenched in liquid nitrogen
    • Sample_growth_protocol_ch1: Chemostat cultivation
    • Sample_growth_protocol_ch1: Strains CEN.PK113-7D were grown at 30°C in 2 liter (L) chemostats (Applikon) with a working volume of 1.0 L. Cultures were fed with a defined mineral medium that limited growth by glucose (C-limited) with all other growth requirements in excess and at a constant residual concentration. Strain Orange02 was grown on synthetic medium, containing 7,5 g L-1 glucose supplemented with 9.38 mM ethanol to avoid metabolic oscillations.. The dilution rate was set at 0.10 h-1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2 M KOH with the use of an Applikon ADI 1030 bio controller. Stirrer speed was 800 rpm, and the airflow was 0.5 L min-1. Dissolved oxygen tension was measured on line with an Ingold model 34-100-3002 probe and was above 50% of air saturation. The off-gas was cooled by a condenser connected to a cryostat set at 2°C, and oxygen and carbon dioxide were measured off-line with an NGA 2000 Rosemount gas analyzer. Steady-state samples were taken after ~10-14 volume changes to avoid strain adaptation due to long term cultivation. Dry weight, glucose and ethanol levels, dissolved oxygen and gas profiles had to be constant over at least 3 volume changes before sampling for RNA extraction.
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Microarray analysis
    • Sample_extract_protocol_ch1: Sampling of strain CEN.PK113-7D from aerobic C-limited chemostats with glucose/ethanol mixture, probe preparation and hybridization to Affymetrix GeneChip microarrays was performed as described previously (Piper et al., 2002), but with the following modifications: Double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix). Double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix). Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA. The results for each growth condition were derived from three or more independently cultured replicates.
    • Sample_extract_protocol_ch1: Piper, M. D., P. Daran-Lapujade, C. Bro, B. Regenberg, S. Knudsen, J. Nielsen, and J. T. Pronk. 2002. Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem. 277:37001-8
    • Sample_label_ch1: SAPE (Phycoerythrin)
    • Sample_label_protocol_ch1: Microarray analysis
    • Sample_label_protocol_ch1: Sampling of strain CEN.PK113-7D from aerobic C-limited chemostats with glucose/ethanol mixture, probe preparation and hybridization to Affymetrix GeneChip microarrays was performed as described previously (Piper et al., 2002), but with the following modifications: Double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix). Double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix). Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA. The results for each growth condition were derived from three or more independently cultured replicates.
    • Sample_label_protocol_ch1: Piper, M. D., P. Daran-Lapujade, C. Bro, B. Regenberg, S. Knudsen, J. Nielsen, and J. T. Pronk. 2002. Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem. 277:37001-8
    • Sample_hyb_protocol: Microarray analysis
    • Sample_hyb_protocol: Sampling of strain CEN.PK113-7D from aerobic C-limited chemostats with glucose/ethanol mixture, probe preparation and hybridization to Affymetrix GeneChip microarrays was performed as described previously (Piper et al., 2002), but with the following modifications: Double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix). Double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix). Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA. The results for each growth condition were derived from three or more independently cultured replicates.
    • Sample_hyb_protocol: Piper, M. D., P. Daran-Lapujade, C. Bro, B. Regenberg, S. Knudsen, J. Nielsen, and J. T. Pronk. 2002. Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem. 277:37001-8
    • Sample_scan_protocol: Affymetrix scanner 3000
    • Sample_description: R08
    • Sample_data_processing: Affymetrix GCOS version 2.1 CHIP 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/GSM209nnn/GSM209979/GSM209979.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM209nnn/GSM209979/GSM209979.EXP.gz
    • Sample_series_id: GSE8451
    • 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: CENPK113-7D glucose/ethanol limited chemostat -2
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.2 3 A
    AFFX-MurIL10_at 0.3 0.8 A
    AFFX-MurIL4_at 1 4.4 A
    AFFX-MurFAS_at 2.5 4.3 A
    AFFX-BioB-5_at 77.3 32.2 P
    AFFX-BioB-M_at 90.6 47 P
    AFFX-BioB-3_at 89 47.6 P
    AFFX-BioC-5_at 156.8 112.8 P
    AFFX-BioC-3_at 153 108.6 P
    AFFX-BioDn-5_at 284 239.4 P
    View Full Table






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