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Sample GSM320335 Query DataSets for GSM320335
Status Public on Feb 28, 2010
Title Patient with BC #4: bronchial carcinoma
Sample type RNA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics bronchial carcinoma
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 41.49191558
ILMN_1833258 28.35651345
ILMN_1714952 39.36324023
ILMN_1687193 35.95633977
ILMN_1882087 42.0502807
ILMN_1915050 38.43838698
ILMN_1817473 42.68182035
ILMN_1875644 44.68666384
ILMN_1839320 45.83901895
ILMN_1763196 39.94054291
ILMN_1799335 50.50253128
ILMN_1671748 37.02957128
ILMN_1865290 38.04202291
ILMN_1750173 42.34855291
ILMN_1687508 50.20206895
ILMN_1828625 46.53665256
ILMN_1853344 39.50021209
ILMN_1869877 47.45106407
ILMN_1789641 45.59099105
ILMN_1916616 46.92435907

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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