1 sample(s) found by the keyword GSM291100.


  1. GEO sample ID: GSM291100
    • Sample_geo_accession: GSM291100
    • Sample_status: Public on Feb 05 2009
    • Sample_submission_date: May 26 2008
    • Sample_last_update_date: Feb 05 2009
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: chemostat culture
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Strain and Maintenance—
    • Sample_characteristics_ch1: This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., and Pronk, J. T. (2000) Enz. Microb. Technol. 26, 706–714]
    • Sample_biomaterial_provider_ch1: SL Tai
    • Sample_treatment_protocol_ch1: Liquid nitrogen quenching
    • Sample_growth_protocol_ch1: Chemostat Cultivation—
    • Sample_growth_protocol_ch1: Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953–28959]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. For anaerobic cultivation, the reservoir medium was supplemented with Tween 80 and ergosterol as described previously. Anaerobic conditions were maintained by sparging the medium reservoir and the fermentor with pure nitrogen gas (0.5 liter_min_1). Furthermore, Norprene tubing and butyl rubber septa were used to minimize oxygen of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.
    • Sample_growth_protocol_ch1: Media—
    • Sample_growth_protocol_ch1: The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. For carbon limited cultivation: 5.0 g of methionine 11.3 g of methionine, 3.0 g of KH2PO4, 0.5 g of MgSO4.7H2O, and 25 g of glucose.
    • Sample_molecule_ch1: polyA RNA
    • Sample_extract_protocol_ch1: Sampling and RNA Isolation—
    • Sample_extract_protocol_ch1: Samples from the chemostat cultures were taken as rapidly as possible to limit any potential changes in transcript profiles during the procedure. 40–60 ml of culture broth was sampled directly from the chemostat into a beaker containing 200 ml of liquid nitrogen. With vigorous stirring, the sample froze instantly. The frozen sample was then broken into small fragments and transferred to a 50-ml centrifuge tube. The sample was then thawed at room temperature, ensuring that it remained as close to zero as possible. Cells were pelleted (5000 rpm at 0 °C for 4 min), resuspended in 2 ml of ice-cold AE buffer (50 mM sodium acetate, 10 mM EDTA, pH 5.0) and aliquoted into 5 Eppendorf tubes. This corresponded to _20 mg of dry weight per tube. For each array, total RNA was extracted from a single tube using the hot-phenol method (32) or the FastRNA kit, Red (BIO 101, Inc., Vista, CA).
    • Sample_label_ch1: Biotinylated dUTP - streptavidine Phycoerythrin (SAPE)
    • Sample_label_protocol_ch1: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.
    • Sample_hyb_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.
    • Sample_scan_protocol: scanning with the Affymetrix GeneArray Scanner.
    • Sample_description: S09.2
    • Sample_data_processing: Data Acquisition and Primary Analysis—Acquisition and quantification
    • 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/GSM291nnn/GSM291100/GSM291100.CEL.gz
    • 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: Anaerobic carbon limited with methionine as N-source -2
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.2 0.9 A
    AFFX-MurIL10_at 0.5 0.5 A
    AFFX-MurIL4_at 2.3 1.8 A
    AFFX-MurFAS_at 3.8 1.9 A
    AFFX-BioB-5_at 100.4 60.4 P
    AFFX-BioB-M_at 126.8 89.1 P
    AFFX-BioB-3_at 99.9 65.9 P
    AFFX-BioC-5_at 155.0 119.5 P
    AFFX-BioC-3_at 144.8 108.3 P
    AFFX-BioDn-5_at 138.4 102.7 P
    View Full Table






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