1 sample(s) found by the keyword GSM29927.


  1. GEO sample ID: GSM29927
    • Sample_geo_accession: GSM29927
    • Sample_status: Public on Sep 03 2004
    • Sample_submission_date: Sep 02 2004
    • Sample_last_update_date: Oct 09 2008
    • 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: V Boer
    • 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. 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_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]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level . For phosphorus-limited, the composition was 5.0 g of (NH4)2SO4, 1.9 g of K2SO4, 0.12 g of KH2PO4, 0.5 g of MgSO4_7H2O, and 59 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: M52.1
    • Sample_description: Keywords
    • Sample_description: Keywords
    • Sample_description: Keywords
    • Sample_data_processing: Data Acquisition and Primary Analysis—Acquisition and quantification
    • Sample_data_processing: 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 4.0.1), 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_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/GSM29nnn/GSM29927/GSM29927.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM29nnn/GSM29927/GSM29927.EXP.gz
    • Sample_series_id: GSE1723
    • Sample_series_id: GSE4807
    • 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 sulfur limited 1
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.2 0.7 A
    AFFX-MurIL10_at 0.3 0.5 A
    AFFX-MurIL4_at 1.3 0.8 A
    AFFX-MurFAS_at 4.3 4.9 A
    AFFX-BioB-5_at 137.7 93.2 P
    AFFX-BioB-M_at 148.7 109.6 P
    AFFX-BioB-3_at 137 98.7 P
    AFFX-BioC-5_at 234.6 196.6 P
    AFFX-BioC-3_at 229.3 189.6 P
    AFFX-BioDn-5_at 210.7 172.3 P
    View Full Table






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