1 sample(s) found by the keyword GSM323161.

  1. GEO sample ID: GSM323161
    • Sample_geo_accession: GSM323161
    • Sample_status: Public on Sep 24 2008
    • Sample_submission_date: Sep 23 2008
    • Sample_last_update_date: Sep 23 2008
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Saccharomyces cerevisiae VTT-C-99318 grown on 50 g/L xylose for 72h
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: CEN.PK2-1D ura3::XYL1 XYL2 his3::XKS1 kanMX
    • Sample_biomaterial_provider_ch1: Technical Research Centre of Finland
    • Sample_treatment_protocol_ch1: The 25 ml sample for transcriptome analysis was harvested by centrifugation (2 min., 5000g) after 5 h growth and frozen in liquid nitrogen.
    • Sample_growth_protocol_ch1: VTT-C-99318 was grown at 30°C in 1.8-litre bioreactors (Chemap CMF Bioreactor, Chemap AG, Volketswil, Switzerland) with a working volume of 1.5 litres. The pH was kept constant at 5.5 by automatic addition of 2M KOH, and the stirrer speed was maintained at 500 rpm. Mass flow controllers (Bronkhorst High-Tech B.V, Ruurlo, Netherlands) regulated the total gas flow rate, at 0.5 standard litres per minute (SLPM). The composition of the fermentor off-gas was analysed using a QMG 421C quadrupole mass spectrometer (Balzers Pfeiffer Scandinavia AB, Sweden). The medium was synthetic complete (modified from Sherman, 1983) supplemented with 0.5 ml silicone antifoam l-1 (AnalaR BDH, UK) and 50 g l-1 xylose. Triplicate cultures (F0, F1, and F2) were carried out. Cultures were started with an initial OD600 of 1 to 1.5.
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Cells were broken by glass beads in the Trizol reagent (Gibco BRL, Life Technologies, USA). After the extraction, RNA was precipitated by isopropyl alcohol and the RNA pellet was rinsed with 80% (v/v) ethanol and resuspended in RNAse-free water.
    • Sample_label_ch1: Biotin
    • Sample_label_protocol_ch1: Affymetrix hybridisations and analyses were carried out according to the protocols provided by Affymetrix, Inc. Double-stranded cDNA was synthesised from 5 µg total RNA. An in vitro transcription (IVT) reaction was then carried out to produce biotin-labelled cRNA from the cDNA. The cRNA was fragmented and hybridised to a Test3 array for quality control, then to the Yeast Genome S98 array for 16 h at 45oC. The arrays were washed and stained with streptavidin-phycoerythrin in an Affymetrix Fluidics Station 400 and scanned (Agilent G2500A GeneArray Scanner). The data were extracted with Affymetrix MicroArray Suite 5.0 software.
    • Sample_hyb_protocol: Affymetrix hybridisations and analyses were carried out according to the protocols provided by Affymetrix, Inc.
    • Sample_scan_protocol: The arrays were scanned by Agilent G2500A GeneArray Scanner.
    • Sample_description: -
    • Sample_data_processing: The data were extracted with Affymetrix MicroArray Suite 5.0 software.
    • Sample_platform_id: GPL90
    • Sample_contact_name: Laura,,Salusjärvi
    • Sample_contact_email: laura.salusjarvi@vtt.fi
    • Sample_contact_institute: VTT Technical Research Centre of Finland
    • Sample_contact_address: Tietotie 2
    • Sample_contact_city: Espoo
    • Sample_contact_zip/postal_code: 02044
    • Sample_contact_country: Finland
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM323nnn/GSM323161/GSM323161.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM323nnn/GSM323161/GSM323161.CHP.gz
    • Sample_series_id: GSE12890
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: VTT-C-99318_fermentation 2_hybridization 2.2_xylose_72h
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.0478069 1.07153 A
    AFFX-MurIL10_at 0.177111 0.349711 A
    AFFX-MurIL4_at 0.636571 0.0702075 A
    AFFX-MurFAS_at 1.31426 0.141108 A
    AFFX-BioB-5_at 24.9571 11.2414 P
    AFFX-BioB-M_at 31.8788 18.4051 P
    AFFX-BioB-3_at 30.9389 17.9581 P
    AFFX-BioC-5_at 44.0062 30.8497 P
    AFFX-BioC-3_at 38.0074 25.2127 P
    AFFX-BioDn-5_at 41.7053 29.3944 P
    View Full Table

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