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Sample GSM320361 Query DataSets for GSM320361
Status Public on Feb 28, 2010
Title Patient without BC #8: control
Sample type RNA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics control
Extracted molecule total RNA
Extraction protocol weWe 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 GPL6102
Series (1)
GSE12771 Lung cancer prediction

Data table header descriptions
ID_REF
VALUE Normalized Value

Data table
ID_REF VALUE
ILMN_1816125 39.60296314
ILMN_1833258 40.93914814
ILMN_1714952 39.61080756
ILMN_1687193 42.16983535
ILMN_1882087 46.34962256
ILMN_1915050 39.99717465
ILMN_1817473 44.81770291
ILMN_1875644 35.28342663
ILMN_1839320 44.98236895
ILMN_1763196 38.28376279
ILMN_1799335 42.12250616
ILMN_1671748 37.24661814
ILMN_1865290 35.00265023
ILMN_1750173 37.0901693
ILMN_1687508 41.53867558
ILMN_1828625 38.5348707
ILMN_1853344 42.01573081
ILMN_1869877 37.57354523
ILMN_1789641 38.19650174
ILMN_1916616 46.71217651

Total number of rows: 48702

Table truncated, full table size 1181 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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