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Sample GSM410840 Query DataSets for GSM410840
Status Public on Jun 02, 2009
Title Prop_30h_A
Sample type RNA
Source name propagation, 30h
Organism Saccharomyces pastorianus
Characteristics strain: CB11
timepoint: 30 hours
Treatment protocol yeast sampling: Triplicate samples of the lager yeast strain CB11 were sampled from a 140 hl (14,000 l) propagation vessel immediately after inoculation and at intervals throughout a 30-hour propagation period. The yeast batch was incubated aerobically in an 8 hl propagation vessel prior to incubation in the principal (140 hl) vessel. Propagation wort (80% malt and 20% maltose adjunct) supplement_protocoled to 0.5 mg l-1 Zn2+ (added as zinc sulphate heptahydrate) and was oxygenated with a ramped supply of molecular oxygen (5-100 l min-1) to give a constant dissolved oxygen concentration of 7-8 mg l-1. Temperature of the wort was maintained throughout at 20°C. Specific gravity of the wort was 17° Plato. Cells and wort were separated by centrifugation at 4°C. Cell pellets for RNA extraction were flash-frozen in liquid nitrogen and stored at -80°C until required.
Extracted molecule total RNA
Extraction protocol RNA extraction was carried out following the method of Lyne et al. RNA yield and purity were determined using an Agilent 2100 Bioanalyser (Agilent Technologies Inc., Santa Clara, California).
Label biotin
Label protocol Biotinylated cRNA was prepared from total RNA with Affymetrix GeneChip Labeling and Control Reagents.
Hybridization protocol Hybridization, washing, staining procedures were conducted with Affymetrix Fluidics Station as described in the Affymetrix GeneChip Expression Analysis Technical Manual.
Scan protocol Scanning done with GeneChip Scanner as described in the Affymetrix GeneChip Expression Analysis Technical Manual.
Description S. pastorianus 30hrs
Data processing CEL files were generated using the GeneChip® operating system (GCOS version 5.0; Affymetrix). The data were analyzed with Affymetrix MAS5 software.
Submission date Jun 01, 2009
Last update date Jun 01, 2009
Contact name Nottingham Arabidopsis Stock Centre (NASC)
Phone +44 (0)115 951 3237
Fax +44 (0)115 951 3297
Organization name Nottingham Arabidopsis Stock Centre (NASC)
Department School of Biosciences, University of Nottingham
Street address Sutton Bonington Campus
City Loughborough
ZIP/Postal code LE12 5RD
Country United Kingdom
Platform ID GPL2529
Series (1)
GSE16376 Differential yeast gene transcription during brewery propagation

Data table header descriptions
VALUE MAS5-calculated signal intensity
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE p-value that indicates the significance level of the detection call

Data table
AFFX-BioB-5_at 303.931 P 7.00668e-05
AFFX-BioB-M_at 334.215 P 4.42873e-05
AFFX-BioB-3_at 351.504 P 4.42873e-05
AFFX-BioC-5_at 713.078 P 5.16732e-05
AFFX-BioC-3_at 841.793 P 4.42873e-05
AFFX-BioDn-5_at 1121.09 P 4.42873e-05
AFFX-BioDn-3_at 3712.56 P 4.42873e-05
AFFX-CreX-5_at 7512.59 P 5.16732e-05
AFFX-CreX-3_at 8838.93 P 4.42873e-05
AFFX-DapX-5_at 3.45281 A 0.327079
AFFX-DapX-M_at 6.746 A 0.287743
AFFX-DapX-3_at 0.624163 A 0.932322
AFFX-LysX-5_at 0.413081 A 0.81489
AFFX-LysX-M_at 0.99474 A 0.824672
AFFX-LysX-3_at 1.40602 A 0.368438
AFFX-PheX-5_at 0.561919 A 0.960339
AFFX-PheX-M_at 0.295025 A 0.9273
AFFX-PheX-3_at 1.005 A 0.904333
AFFX-ThrX-5_at 1.12855 A 0.949771
AFFX-ThrX-M_at 6.90204 A 0.165861

Total number of rows: 10928

Table truncated, full table size 333 Kbytes.

Supplementary file Size Download File type/resource
GSM410840.CEL.gz 785.0 Kb (ftp)(http) CEL
GSM410840.CHP.gz 2.4 Mb (ftp)(http) CHP
GSM410840.RPT.gz 1018 b (ftp)(http) RPT
Processed data included within Sample table
Processed data provided as supplementary file

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