|
| Status |
Public on Oct 30, 2008 |
| Title |
array-CGH - GBM5 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
GBM5 - tumor DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Age: 75; Gender: Male; WHO grade IV
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with Macherey Nagel NucleoSpin Tissue Kit. The quantification of DNA was done by spectrophotometry (Nanodrop, Labtech); integrity and purity were analyzed on 1% agarose gel.
|
| Label |
Cy3
|
| Label protocol |
5microg DNA were double-digested with AluI and RsaI (Promega, Madison, WI, USA) for 2h at 37C. The digested DNA was labeled by random priming using the Bioprime DNA Labeling Kit (Invitrogen, Carlsbad, USA). DNA was labeled with Cy3-dUTP (PerkinElmer, Waltham, USA) . Labeled product was purified with Microcon YM (Millipore, Billerica, MA, USA).
|
| |
|
| Channel 2 |
| Source name |
GBM5 - blood DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Age: 75; Gender: Male; WHO grade IV
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Classical saline extraction from peripheral blood leucocytes. The quantification of DNA was done by spectrophotometry (Nanodrop, Labtech); integrity and purity were analyzed on 1% agarose gel.
|
| Label |
Cy5
|
| Label protocol |
5microg DNA were double-digested with AluI and RsaI (Promega, Madison, WI, USA) for 2h at 37C. The digested DNA was labeled by random priming using the Bioprime DNA Labeling Kit (Invitrogen, Carlsbad, USA). DNA was labeled with Cy3-dUTP (PerkinElmer, Waltham, USA) . Labeled product was purified with Microcon YM (Millipore, Billerica, MA, USA).
|
| |
|
| |
| Hybridization protocol |
Tumor and control DNAs were pooled and hybridized with 50microg of Human Cot I DNA at 65°C with rotation for 48 hours. Washing was performed according to the Agilent protocol.
|
| Scan protocol |
Arrays were analyzed using the Agilent G2565BA microarray scanner and the Feature Extraction software (FE v9.4.1, CGH_44k_1005 protocol).
|
| Description |
Low quality spots were flagged according to default FE criteria and corresponding values were removed.
|
| Data processing |
Data preprocessing was carried out using limma (R package) from Bioconductor with adaptation to array CGH data files. Quality control was performed by visualization of the spatial distribution of probes; background array images and examination of boxplots, histograms, global MvA plots and per chromosome MvA plots. Median pixel feature intensity values were median normalized. 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 |
GPL2879 |
| Series (1) |
| GSE10878 |
Integrative Genome-wide Analysis of Glioblastoma. |
|
