1 sample(s) found by the keyword GSM211831.


  1. GEO sample ID: GSM211831
    • Sample_geo_accession: GSM211831
    • 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 1 hour
    • 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 1 hour
    • 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/GSM211831/GSM211831.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: 1 hour rep 2
    ID_REF Corrected Value VALUE
    10000_at 3.05767594784013 3.27790043129261
    10001_at 7.73908349320977 7.77484187930866
    10002_i_at 10.4100023623458 10.3713112779557
    10003_f_at 12.0001219779472 11.9691361169638
    10004_at 3.26085447916072 3.52447667892498
    10005_at 7.21568339795246 7.33552794975626
    10006_at 7.37674610085325 7.52529603860078
    10007_at 5.30211759666742 5.5745742214195
    10008_at 4.66778313906826 5.00512950661383
    10009_at 5.17865847906179 5.43815443786187
    View Full Table






Developed by Dirar Homouz, Gang Chen, and Andrzej S. Kudlicki*

Software download