1 sample(s) found by the keyword GSM243575.


  1. GEO sample ID: GSM243575
    • Sample_geo_accession: GSM243575
    • Sample_status: Public on Jun 09 2008
    • Sample_submission_date: Nov 19 2007
    • Sample_last_update_date: Jun 09 2008
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Steady State SAmple
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: strain: sfp1Δ; genotype: MATa MAL2-8c SUC2 leu2-3,112 sfp1Δ::KlLEU2
    • Sample_biomaterial_provider_ch1: Chiara Cipollina
    • Sample_treatment_protocol_ch1: liquid nitrogen quenching
    • Sample_growth_protocol_ch1: The S. cerevisiae sfp1 null mutant (MATa MAL2-8c SUC2 leu2-3,112 sfp1Δ::KlLEU2) was grown at 30 °C in 2-l bioreactors with a working volume of 1.5 l. Removal of effluent from the center of the culture ensured that biomass concentrations in the effluent line differed by less than 1% from those in the culture. The dilution rate was set at 0.10 h-1. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. A stirrer speed of 800 rpm and air flow of 0.75 liter•min-1 were applied to keep the dissolved-oxygen concentration, as measured with an oxygen electrode, above 60% of air saturation in all chemostat cultivations performed. Steady-state samples were taken after 10 volume changes to avoid strain adaptation due to long-term cultivation. Biomass dry weight, metabolite, dissolved oxygen, and gas profiles were constant over at least three volume changes.
    • Sample_growth_protocol_ch1: Anaerobic glucose-pulse experiments were started by sparging the medium reservoir of a steady-state glucose-limited aerobic chemostat (airflow of 0.5 liter•min-1) with pure nitrogen gas. Norprene tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic cultures. Two min after nitrogen sparging and just before adding the glucose, the medium pump was switched off. The 200 mM glucose pulse was injected aseptically through a rubber septum. Samples for RNA extraction were taken at 5, 10, 30, 60 and 120 minutes after the perturbation from two independently cultured replicates, while steady state data were taken from three independent chemostats.
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Sampling of cells from chemostats and total RNA extraction was performed as previously described (1).
    • Sample_extract_protocol_ch1: (1). Abbott, D. A., T. A. Knijnenburg, L. M. de Poorter, M. J. Reinders, J. T. Pronk, and A. J. van Maris. 2007. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res.
    • Sample_label_ch1: Biotynylated -UTP + SAPE
    • Sample_label_protocol_ch1: EukGE-ws2v4
    • Sample_hyb_protocol: Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies) (1).
    • Sample_hyb_protocol: (1). Abbott, D. A., T. A. Knijnenburg, L. M. de Poorter, M. J. Reinders, J. T. Pronk, and A. J. van Maris. 2007. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res.
    • Sample_scan_protocol: Affymetrix scanner 3000
    • Sample_description: ES30
    • Sample_data_processing: GeneChip® Operating Software (GCOS), version 1.2
    • Sample_platform_id: GPL90
    • Sample_contact_name: Chiara,,Cipollina
    • Sample_contact_email: c.cipollina@tudelft.nl
    • Sample_contact_department: Biotechnology
    • Sample_contact_institute: Delft University of Technology
    • Sample_contact_address: Julianalaan 67
    • Sample_contact_city: Delft
    • Sample_contact_zip/postal_code: 2628 BC
    • Sample_contact_country: Netherlands
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM243nnn/GSM243575/GSM243575.CEL.gz
    • Sample_series_id: GSE9644
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Steady-state based anaerobic glucose pulse, sfp1delta_SS_1
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.1 0.3 A
    AFFX-MurIL10_at 0.2 0.3 A
    AFFX-MurIL4_at 1.3 0.3 A
    AFFX-MurFAS_at 3.1 0.4 A
    AFFX-BioB-5_at 66.6 24.9 P
    AFFX-BioB-M_at 81.6 39.9 P
    AFFX-BioB-3_at 82.3 41.5 P
    AFFX-BioC-5_at 117.2 76 P
    AFFX-BioC-3_at 115 73.6 P
    AFFX-BioDn-5_at 198.6 155.6 P
    View Full Table






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