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Sample GSM320357 Query DataSets for GSM320357
Status Public on Feb 28, 2010
Title Patient with BC #33: 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 30.60314278
ILMN_1833258 33.00982194
ILMN_1714952 35.59532
ILMN_1687193 34.73428306
ILMN_1882087 39.23481361
ILMN_1915050 39.88988806
ILMN_1817473 38.89869361
ILMN_1875644 37.07905833
ILMN_1839320 45.26371361
ILMN_1763196 42.38418306
ILMN_1799335 37.76352694
ILMN_1671748 40.29910194
ILMN_1865290 35.69882056
ILMN_1750173 36.89559333
ILMN_1687508 44.18153778
ILMN_1828625 37.48789667
ILMN_1853344 33.14309306
ILMN_1869877 35.06349889
ILMN_1789641 36.39447861
ILMN_1916616 41.33817444

Total number of rows: 48702

Table truncated, full table size 1179 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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