|
| Status |
Public on Dec 19, 2007 |
| Title |
GL4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
low grade brain tumor pool
|
| Organism |
Homo sapiens |
| Characteristics |
pool of 4 oligodendrogliomas(OL), 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytomas (FA)
|
| Biomaterial provider |
Luca Morandi
|
| Treatment protocol |
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S:1.66
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Protect RNAeasy Mini kit protocol (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
The labeled cRNA was generated by in vitro transcription with the use of T7 RNA polymerase (low RNA input fluorescent linear amplification kit Agilent cod. 5184-3523).
|
| |
|
| Channel 2 |
| Source name |
GL4
|
| Organism |
Homo sapiens |
| Characteristics |
Fresh frozen biopsy from left cerebellar of a 40 years old men. Overall Survival (months): 1.5
|
| Biomaterial provider |
Luca Morandi
|
| Treatment protocol |
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S: 1.29
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Protect RNAeasy Mini kit protocol (Qiagen)
|
| Label |
Cy5
|
| Label protocol |
The labeled cRNA was generated by in vitro transcription with the use of T7 RNA polymerase (low RNA input fluorescent linear amplification kit Agilent cod. 5184-3523).
|
| |
|
| |
| Hybridization protocol |
0.75 ug of labeled test and reference cRNA were fragmented and hybridized at 60 C for 17 hours.
The washing steps were done following the SSC protocol (version 3.0, Agilent)
|
| Scan protocol |
After hybridization and washes, the slides were scanned with a confocal laser scanner (Agilent G2565BA).
|
| Description |
Fluorescent intensities on scanned images were quantified by the feature extraction software 7.5, and LogRatio data were available for further statistical analysis.
|
| Data processing |
The scan data were analysed with Agilent Feature Extraction Software, which performs spots localization (Find Spot Algorhythm), outlier pixels rejection based on the Interquartile Range method (Cookie Cutter Algorhythm), flagging of saturated features (a feature is considered saturated when more than 50% of its pixels had an intensity above 65502). Loess normalization and between array scale normalization were performed using the “LIMMA” package of Bioconductor (www.bioconductor.org).
|
| |
|
| Submission date |
Dec 12, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Luca Morandi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Bologna
|
| Department |
Oncology Dept
|
| Lab |
Anatomia Patologica Bellaria Hospital
|
| Street address |
Via Altura 3
|
| City |
Bologna |
| ZIP/Postal code |
40139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL887 |
| Series (1) |
| GSE9885 |
Gene expression profiling in glioblastoma and immunohistochemical evaluation of IGFBP-2 and CDC20 |
|
