|
| Status |
Public on Oct 30, 2008 |
| Title |
expression microarray - GBM5 |
| Sample type |
RNA |
| |
|
| Source name |
GBM5 - tumor RNA
|
| Organism |
Homo sapiens |
| Characteristics |
Age: 75; Gender: Male; WHO grade IV
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the NucleoSpin RNAII Kit (Macherey-Nagel, Düren, DE) and quantified via spectrophotometry (Nanodrop, Labtech). RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
|
| Label |
Cy3
|
| Label protocol |
Agilent’s recommended procedures for microarray-based one-color gene expression analysis were followed. Briefly, 350ng of total RNA with control RNA Spike In were amplified and labeled with Cy3-CTP using the T7-based Low RNA Input Linear Amplification Kit, PLUS, One-Color (Agilent Technologies, Santa Clara, CA). After purification (RNeasy Mini Kit, QIAGEN), labeled cRNAs were quantified for yield and dye incorporation using a Nanodrop spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65microg of Cy3-labeled RNA were hybridized to each array in a 110microl total volume of hybridization buffer (Agilent Technologies) for 17 hours at 65°C. Washing was performed according to the Agilent protocol.
|
| Scan protocol |
Arrays were analyzed using the dynamic autofocus Agilent G2565BA microarray scanner and the Agilent Feature Extraction software (FE v9.4.1, GE1-v5_91_0806 protocol).
|
| Description |
Poor quality spots were flagged according to default FE criteria and corresponding values were removed.
|
| Data processing |
Median normalization from the processed Multiplicative Detrend FE data was carried out using limma (R package) from Bioconductor. Missing values were imputed by the use of the k-nearest neighbors method implemented in impute (R package).
|
| |
|
| Submission date |
Mar 18, 2008 |
| Last update date |
Sep 20, 2008 |
| Contact name |
Marie de Tayrac |
| E-mail(s) |
marie.de-tayrac@univ-rennes1.fr
|
| Phone |
0223234776
|
| Organization name |
CNRS-UMR6061
|
| Lab |
Regulation of transcription and oncogenesis
|
| Street address |
2 avenue du Professeur Léon Bernard
|
| City |
Rennes |
| ZIP/Postal code |
35000 |
| Country |
France |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE10878 |
Integrative Genome-wide Analysis of Glioblastoma. |
|
