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Sample GSM320434 Query DataSets for GSM320434
Status Public on Feb 28, 2010
Title cosmos sample 14: control
Sample type RNA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics control
Extracted molecule total RNA
Extraction protocol We used snap frozen PBMC enriched blood (~ 300 µl) from the EPIC study for RNA extraction. Blood samples were directly thawed in 5ml of TRI Reagent BD (Molecular Research Center, Inc, USA). RNA was extracted according to the manufactures instruction and stored in 70% ethanol until finalization of preparation and dilution in H2O. For further RNA purification we applied Qiagen MinElute columns (Qiagen, Germany). By this method we extracted 960ng RNA (mean; range 120 – 2500ng). One sample contained no RNA. The OD ratio 260/280 was 2.01 in mean (range 1.76-2.06). For the LC-group, we drew 2.5 ml blood directly into PAXgene vials providing stabilization of the gene expression profile. Samples were rested over night at room temperature and then stored at -80°C until further preparation. RNA was extracted according to the manufactures instruction (Qiagen, Hilden, Germany).
Label biotin
Label protocol Biotin labeled cRNA preparation was performed using the Ambion® Illumina RNA amplification kit (Ambion, UK). Quality was controlled using a PCR based system1.
 
Hybridization protocol For hybridization samples were applied to the arrays and assembled into HybCartridges (Illumina). BeadChips were hybridized for 16h at 55°C on the BeadChip Hyb Wheel. 1.5 μg biotin labeled cRNA was hybridized to Sentrix® whole genome bead chips 6 x 2 V1 and V2 (Illumina, USA) according to the manufacturers instruction. Arrays were washed according to Illumina Wash BeadChip 6 x 2 protocol. Signals were developed with streptavidin Cy3.
Scan protocol Scanning was performed on the Illumina(r) BeadStation 500x
Description All samples were taken from smokers. EPIC cases were taken from the EPIC trial (a large prospective epidemiological trial in Europe, and are incident cases), Cosmos and BC cases are prevalent cases from a Cologne, Germany based epidemiological trial.
Data processing BeadStudio raw data were normalized using R
 
Submission date Sep 13, 2008
Last update date Oct 23, 2009
Contact name Thomas Zander
Organization name University Hospital Cologne
Street address Kerpenerstr. 62
City Cologne
ZIP/Postal code 50924
Country Germany
 
Platform ID GPL6097
Series (1)
GSE12771 Lung cancer prediction

Data table header descriptions
ID_REF
VALUE Normalized Value

Data table
ID_REF VALUE
106520673 62.52916667
102900035 69.68333333
106520368 63.7625
102450204 91.29583333
103520050 65.50833333
104120524 77.39583333
104810600 85.475
105420440 71.85833333
104810735 87.53333333
106760022 65.77083333
106760484 70.90833333
103990066 84.3
106200504 88.73333333
105390279 69.29166667
106350358 69.55416667
104010113 76.42916667
102030332 93.12083333
106520450 77.25
104610142 69.55416667
106760338 73.10833333

Total number of rows: 47296

Table truncated, full table size 906 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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