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Sample GSM320481 Query DataSets for GSM320481
Status Public on Feb 28, 2010
Title epic sample 1: bronchial carcinoma
Sample type RNA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics bronchial carcinoma
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
2360044 109.6861111
3940446 217.0138889
6420736 224.125
2630279 107.7916667
3120162 93.53333333
6900279 123.4361111
1980670 99.69722222
670603 110.9138889
4920152 97.62777778
1240333 2406.469444
6510707 114.0166667
2120377 87.74166667
5570131 198.5083333
4120338 182.85
2190593 109.6861111
1770215 92.46666667
780706 119.4277778
2100458 112.475
2680121 108.8166667
1240112 117.4305556

Total number of rows: 47296

Table truncated, full table size 935 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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