|
| Status |
Public on Nov 13, 2015 |
| Title |
Tumor_129 |
| Sample type |
RNA |
| |
|
| Source name |
female_smoker_tumor
|
| Organism |
Homo sapiens |
| Characteristics |
age (yrs): 58
smoking: Smoker
gender: Female
tissue: Lung adenocarcinoma tissue
Stage: IIIa
tp53 mutation: wild type
egfr mutation: wild type
kras mutation: mutated
|
| Treatment protocol |
Tissue obtained at the surgery were snap frozen in liquid nitrogen and stored at –80°C until DNA and RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard TRIZOL methods (Invitrogen, Carlsbad, CA, USA) were used to extract total RNA and the procedure was done according to manufacturer's instruction.
|
| Label |
Cy3
|
| Label protocol |
Total RNA from each tumor sample (50ng) was converted to cDNA through reverse transcription with the use of a T7-oligo (dT) primer. By using quick-AMP labeling kit (Agilent technologies), amplified and Cy3-labeled cRNA were produced.
|
| |
|
| Hybridization protocol |
The labeled cRNA were hybridized to slides that were incubated for 17 hours at 65°C.
|
| Scan protocol |
Arrays were scanned by using Agilent Microarray Scanner (Agilent technologies) and the raw data were preprocessed with the Agilent's Feature Extraction Software with default parameters (Agilent feature extraction version 10.7.3.1).
|
| Description |
Sample129
|
| Data processing |
The gene expression values were log 2 transformed and normalized between arrays by using the 75th percentile method in Genespring GX analysis Software v.12.1 (Agilent technology).
|
| |
|
| Submission date |
Mar 13, 2015 |
| Last update date |
Nov 13, 2015 |
| Contact name |
Maria Moksnes Bjaanæs |
| E-mail(s) |
maria.moksnes.bjaanas@rr-research.no
|
| Phone |
+4797123468
|
| Organization name |
Oslo Universitetssykehus
|
| Department |
Department of genetics
|
| Street address |
Ullernchausseen 70
|
| City |
Oslo |
| ZIP/Postal code |
0310 |
| Country |
Norway |
| |
|
| Platform ID |
GPL14550 |
| Series (1) |
| GSE66863 |
Genome-wide DNA methylation signature in lung adenocarcinomas has prognostic impact [gene expression] |
|
