1 sample(s) found by the keyword GSM291107.

  1. GEO sample ID: GSM291107
    • Sample_geo_accession: GSM291107
    • 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—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: JM Daran
    • Sample_treatment_protocol_ch1: liquid N2 quenching
    • Sample_growth_protocol_ch1: Chemostat Cultivation—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 medium was supplemented with anaerobic factors (ergosterol and tween 80) as in anaerobic chemostat fermentation.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.Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.
    • Sample_molecule_ch1: polyA RNA
    • Sample_extract_protocol_ch1: Sampling and RNA Isolation—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 UTP
    • 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.
    • Sample_hyb_protocol: 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.(1) Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual, Santa Clara, CA
    • Sample_scan_protocol: Data Acquisition and Primary Analysis—Acquisition and quantification of array images as well as primary data analysis were performed using the Affymetrix software packages: Microarray Suite version 4.0.1, MicroDB version 2.0, and Data Mining Tool version 2.0. Microsoft Excel was used for further statistical analyses. All arrays were globally scaled to a target value of 150 using the average signal from all gene features using Microarray Suite version 4.0.1. When pairwise comparisons were performed (using Microarray Suite version 5.0), a transcript was considered “changed” when a call 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_description: S14
    • Sample_data_processing: MAS 5.0
    • 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/GSM291107/GSM291107.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: Aerobic phosphorus limited chemostat with anaerobic factors (tween and ergosterol) -1
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.2 0.6 A
    AFFX-MurIL10_at 0.3 0.5 A
    AFFX-MurIL4_at 0.8 0.5 A
    AFFX-MurFAS_at 2.1 0.5 A
    AFFX-BioB-5_at 96.1 56.5 P
    AFFX-BioB-M_at 106.2 68.8 P
    AFFX-BioB-3_at 88.2 53.5 P
    AFFX-BioC-5_at 126.2 90.7 P
    AFFX-BioC-3_at 108.3 70.1 P
    AFFX-BioDn-5_at 112.6 74.6 P
    View Full Table

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

Software download