|
| Status |
Public on Oct 13, 2009 |
| Title |
U87MG cell line - rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Human glioblastoma cell line U87MG
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U87MG
|
| Growth protocol |
Human glioblastoma cell lines T98G and U87MG were grown in DMEM supplemented with 10% fetal bovine serum (FBS), penicillin (100U/ml), glutamine (2mmol/L) and streptomycin (100 µg/ml) at 37°C in 5% CO2 atmosphere.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).
|
| Label |
biotin
|
| Label protocol |
A 6μg-amount of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Labeled cRNA was hybridized on Affymetrix GeneChip Human Genome U133A 2.0 Arrays. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).
|
| Scan protocol |
Arrays were scanned with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS).
|
| Description |
U87MG cells are resistant to apoptosis induced by bortezomib and G5 but susceptible to necrosis induced by G5.
|
| Data processing |
Further data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Prior to statistical analysis, normalized data were then filtered based on Affymetrix detection call so that only probes that had a present call in at least one of the arrays were retained. Probes with intensity values <100 in all arrays were also excluded. Statistical analysis was performed with LIMMA. P-values were adjusted for multiple testing using Benjamini and Hochberg’s method to control the false discovery rate. A threshold value of 2-fold change was applied.
|
| |
|
| Submission date |
Feb 18, 2009 |
| Last update date |
Oct 13, 2009 |
| Contact name |
Paola Roncaglia |
| Organization name |
SISSA/ISAS (International School for Advanced Studies)
|
| Department |
Neurobiology
|
| Street address |
via Bonomea 265
|
| City |
Trieste |
| State/province |
TS |
| ZIP/Postal code |
34136 |
| Country |
Italy |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE14889 |
A caspase-independent necrotic death is activated by isopeptidase inhibitor G5 in apoptosis-resistant glioblastoma cells |
|
