|
| Status |
Public on Mar 08, 2013 |
| Title |
GBM pool_5 FFPE biopsies |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DNA pool isolated from 5 FFPE-GBM samples
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 1 pool from 5 GBM biopsies
antibody: 5-methylcytosine
antibody vendor: Eurogentec
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA from cell lines was isolated using the Wizard Genomic DNA Purification Kit (Promega) following manufacturer's instructions. Total DNA from FFPE samples was isolated using Invisorb Spin FFPE Tissue Kit following manufacturer's instructions. 5µg of whole DNA were diluited in 1X PBS (for each sample).
|
| Label |
Cy5
|
| Label protocol |
IP and Total DNA were labeled according to manufacturer's instructions with Cy5 and Cy3 fluorescent dyes, respectively (see manufacturer's web site at http://www.agilent.com/).
|
| |
|
| Channel 2 |
| Source name |
DNA pool isolated from FFPE-GBM samples
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 1 pool from 5 GBM biopsies
sample type: input DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA from cell lines was isolated using the Wizard Genomic DNA Purification Kit (Promega) following manufacturer's instructions. Total DNA from FFPE samples was isolated using Invisorb Spin FFPE Tissue Kit following manufacturer's instructions. 5µg of whole DNA were diluited in 1X PBS (for each sample).
|
| Label |
Cy3
|
| Label protocol |
IP and Total DNA were labeled according to manufacturer's instructions with Cy5 and Cy3 fluorescent dyes, respectively (see manufacturer's web site at http://www.agilent.com/).
|
| |
|
| |
| Hybridization protocol |
Hybridization and wash were performed following Agilent guidelines (see manufacturer's web site at http://www.agilent.com/).
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner. mages were quantified using Agilent Feature Extraction Software (v 10.7.3.1).
|
| Data processing |
Data were processed using Agilent Feature Extraction Software (v 10.7.3.1) and the Agilent Genomic Workbench (v 5.0.14). The algorithm used to obtain z-score values is the Methylation status detection algorithm that is integrated in the Genomic Workbench software (Agilent Technologies). Specifically, as described in the Agilent Methylation (CH3) Analysis User Guide (available at http://www.genomics.agilent.com/files/Manual/G3800-90010_MethylationAnalysis.pdf). The algorithm first bins the probes by their melting temperature. For each bin, it applies Gaussian fits using one of three models. It fits the probe log-ratios to Gaussians, using a local searching algorithm called *random * *hill climbing* *Z*- scores and *p*- values derived from the Gaussian data give probabilities and confidence values for methylated and unmethylated probe populations. Additionally the Z-score represents the number of standard deviations separating the smoothed adjusted log-ratio of a probe from the median of the null probes according to their Tm. The combined Z-score is the combination of both the methylated and unmethylated ZScores. For further information about the algorithm and the Z-core values please refer to the methylation analysis user guide.
|
| |
|
| Submission date |
Oct 24, 2012 |
| Last update date |
Mar 08, 2013 |
| Contact name |
Simona Baronchelli |
| Organization name |
University of Milan-Bicocca
|
| Street address |
Via Cadore 48
|
| City |
Monza |
| ZIP/Postal code |
20900 |
| Country |
Italy |
| |
|
| Platform ID |
GPL9767 |
| Series (1) |
| GSE41824 |
Methylation profiling of Glioma Stem Cell lines vs GBM FFPE tissue biopsies and foetal Neural Stem Cell lines |
|
