1 sample(s) found by the keyword GSM242662.


  1. GEO sample ID: GSM242662
    • Sample_geo_accession: GSM242662
    • Sample_status: Public on Nov 15 2007
    • Sample_submission_date: Nov 13 2007
    • Sample_last_update_date: Nov 15 2007
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: chemostat culture sample
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: CENPK632-3B
    • Sample_characteristics_ch1: MATa MAL2–8c SUC2 ydl080c delta ydr380w::loxP-Kan-loxP
    • Sample_biomaterial_provider_ch1: JM Daran
    • Sample_treatment_protocol_ch1: Treatment protocol Liquid nitrogen quenching
    • Sample_growth_protocol_ch1: Chemostat cultivation.
    • Sample_growth_protocol_ch1: Aerobic chemostat cultivation was performed at 30°C in 1-liter (working volume) laboratory fermentors (Applikon, Schiedam, The Netherlands) at a stirrer speed of 800 rpm and pH 5.0 with a dilution rate of 0.10 h_1. The pH was kept constant by usingan ADI 1030 biocontroller (Applikon) and automatic addition of 2 M KOH. The fermentor was flushed with air at a flow rate of 0.5 liter min_1 by using a Brooks 5876 mass flow controller (Brooks Instruments, Veenendaal, The Netherlands). The dissolved oxygen concentration was continuously monitored with an Ingold model 34 100 3002 probe (Mettler-Toledo, Greifensee, Switzerland) and was more than 50% of air saturation.
    • Sample_growth_protocol_ch1: Carbon-limited steady-state chemostat cultures of both wild-type and mutant strains were grown on the mineral medium described by Verduyn et al. (1) containing 7.5 g of glucose liter_1 as carbon source and 5.0 g of phenylalanine liter_1 as the sole nitrogen source.
    • Sample_growth_protocol_ch1: When phenylalanine was the sole nitrogen source, the amino acid solution was sterilized separately by autoclaving it before addition to the medium, and the absence of (NH4)2SO4 was compensated for by addition of equimolar amounts of K2SO4. For chemostat cultivation of pyruvate decarboxylase-negative strains, 7.1 g of glucose liter_1 and 0.38 g of acetate liter_1 (5% acetate on a carbon basis) were used as carbon sources to overcome the C2 requirement of PDC negative
    • Sample_growth_protocol_ch1: strains (2).
    • Sample_growth_protocol_ch1: 1- Verduyn, C., E. Postma, W. A. Scheffers, and J. P. van Dijken. 1990. Physiology of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures. J. Gen. Microbiol. 136:395–403.
    • Sample_growth_protocol_ch1: 2- Flikweert, M. T., L. Van Der Zanden, W. M. Janssen, H. Y. Steensma, J. P. van Dijken, and J. T. Pronk. 1996. Pyruvate decarboxylase: an indispensable enzyme for growth of Saccharomyces cerevisiae on glucose. Yeast 12:247–257.
    • Sample_molecule_ch1: polyA RNA
    • Sample_extract_protocol_ch1: Extracted molecule polyA RNA Extraction protocol 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 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. 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 . Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.
    • Sample_hyb_protocol: Hybridization 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: Scan protocol Scanning with the Affymetrix GeneArray Scanner.
    • Sample_description: M60
    • Sample_data_processing: MAS5
    • 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/GSM242nnn/GSM242662/GSM242662.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM242nnn/GSM242662/GSM242662.EXP.gz
    • Sample_series_id: GSE9590
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: aro10delta thi3delta strain glc-limited chemostat with phenylalanine -1
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.2 0.6 A
    AFFX-MurIL10_at 0.2 0.3 A
    AFFX-MurIL4_at 0.5 0.9 A
    AFFX-MurFAS_at 3.2 4.8 A
    AFFX-BioB-5_at 131.4 88.1 P
    AFFX-BioB-M_at 241.8 200.8 P
    AFFX-BioB-3_at 190.7 149.0 P
    AFFX-BioC-5_at 277.9 241.4 P
    AFFX-BioC-3_at 237.4 200.7 P
    AFFX-BioDn-5_at 289.5 255.0 P
    View Full Table






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