1 sample(s) found by the keyword GSM211844.


  1. GEO sample ID: GSM211844
    • Sample_geo_accession: GSM211844
    • Sample_status: Public on Apr 17 2008
    • Sample_submission_date: Jul 20 2007
    • Sample_last_update_date: Apr 16 2008
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: yeast cells harvested after 60 hours
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: An industrial wine strain of S. cerevisiae, Vin13 (Anchor Yeast, South Africa), was used. The dried yeast was resuspended (Marks et al, 2003) and inoculated into 1 L filter sterilized Riesling grape juice harvested from the Okanagan Valley in British Columbia, Canada in the 2000 growing season. The final cell count was 4 x 106 /ml. The grape juice contained 214 g/L sugar (equimolar amounts of glucose and fructose), 70 mg/ L ammonia, and 140 mg/L free alpha-amino nitrogen (Marks, 2003 et al, 2003). Incubation was at 20 °C
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: extraction of total RNA was done according to (Causton et al, Mol. Biol. Cell 12, 323–337,2001). Double-stranded cDNA was purified using phenol/chloroform/isoamyl alcohol (25:24:1) saturated with 10 mM Tris–HCl, pH 8.0, 1 mM EDTA (Ambion, Austin, TX, USA) and a Phase Lock Gel prepared according to the manufacturer's instructions (Eppendorf, Hamburg, Germany)
    • Sample_label_ch1: biotin
    • Sample_label_protocol_ch1: Following ethanol precipitation, cRNA was prepared by in vitro transcription of the cDNA using the Enzo BioArray™ HighYield™ RNA Transcript Labeling kit (Farmingdale, NY, USA). The cRNA was purified with RNeasy spin columns (Qiagen, Mississauga, ON, Canada), followed by ethanol precipitation. Then, 20 μg of cRNA (0.5 μg μl-1) was fragmented by incubating at 94°C for 35 min in fragmentation buffer (40 mM Tris–acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate). Further details of procedures can be found in the GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA, USA).
    • Sample_hyb_protocol: 20 μg of cRNA (0.5 μg μl-1) was fragmented by incubating at 94°C for 35 min in fragmentation buffer (40 mM Tris–acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate)
    • Sample_scan_protocol: as described by the manufacturer (Eukaryotic Arrays GeneChip Expression Analysis and Technical Manual, Affymetrix, Santa Clara, CA), using an Agilent G2500A GeneArray Scanner
    • Sample_description: yeast cells harvested after 60 hours
    • Sample_data_processing: RMA applied to the whole series (as implemented in the 'affy' package in Bioconductor)
    • Sample_platform_id: GPL90
    • Sample_contact_name: Hennie,JJ,van Vuuren
    • Sample_contact_email: hjjvv@interchange.ubc.ca
    • Sample_contact_phone: (604) 822-0418
    • Sample_contact_fax: (604) 822-5143
    • Sample_contact_institute: UBC
    • Sample_contact_address: 2205 East Mall
    • Sample_contact_city: Vancouver
    • Sample_contact_state: BC
    • Sample_contact_zip/postal_code: V6T 1Z4
    • Sample_contact_country: Canada
    • Sample_contact_web_link: http://www.landfood.ubc.ca/wine/
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM211nnn/GSM211844/GSM211844.CEL.gz
    • Sample_series_id: GSE8536
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: 60 hour rep 3
    ID_REF Corrected Value VALUE
    10000_at 2.91931534168222 3.22544305593973
    10001_at 6.80332559037808 6.83815416387822
    10002_i_at 10.0451003040734 10.0946511807347
    10003_f_at 11.0812109987874 11.0822349094825
    10004_at 3.01914838021414 3.29555723412488
    10005_at 6.45517082393296 6.55473142207292
    10006_at 6.21693781934716 6.39073559446807
    10007_at 6.89799143118671 7.08714216494225
    10008_at 6.02615854397346 6.2174724010893
    10009_at 4.83199507053052 5.06207813730731
    View Full Table






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