|
| Status |
Public on Oct 07, 2014 |
| Title |
A612_02_R40_DMSO_GF |
| Sample type |
RNA |
| |
|
| Source name |
brain tumor initiating cells (BTIC)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: brain tumor initiating cells (BTIC)
treatment: DMSO
gf: yes
btic culture: BTIC_3
|
| Treatment protocol |
Cells were cultured in growth factor free medium for 16 hours prior to treatment. After starvation, cells were treated with 1 µM Sunitinib in the treatment groups or 0.00025 % DMSO in the control groups either with or without supplementation of recombinant growth factors PDGF-A/B and VEGFA (25 ng/ml) for 6 hours before harvest.
|
| Growth protocol |
BTICs were cultured in stem-cell permissive RHB-A media (Stem Cell, Cambridge, UK) supplemented with 20 ng/ml of each human recombinant epidermal growth factor (EGF; R&D Systems, Minneapolis, USA) and human recombinant basic fibroblast growth factor (FGF; Peprotech, Hamburg, Germany).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed twice with ice-cold PBS and harvested in RLT-lysis buffer (provided in the RNeasy Kit, Qiagen, Hilden, Germany) for subsequent RNA-extraction
|
| Label |
biotin
|
| Label protocol |
cRNA and ssDNA were prepared from 0.3 µg totalRNA according to the Ambion WT Expression Kit manual. Fragmentation and terminal biotinylation were performed using the Affymetrix Terminal Labeling Kit.
|
| |
|
| Hybridization protocol |
3 μg of labelled products were hybridized, washed and stained in an Affymetrix GeneTitan system.
|
| Scan protocol |
Arrays were scanned in an Affymetrix GeneTitan system.
|
| Data processing |
Raw intensities were quantile normalized and summarized with the RMA (Robust Multichip Average) expression measure described in Irizarry et al, Biostatistics (2003)
For the final analysis, only those features were used that could be mapped to EntrezIDs.
|
| |
|
| Submission date |
Sep 30, 2013 |
| Last update date |
Oct 08, 2014 |
| Contact name |
Christian W Kohler |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Regensburg
|
| Department |
Institute of Functional Genomics
|
| Lab |
Statistical Bioinformatics
|
| Street address |
Am BioPark 9
|
| City |
Regensburg |
| State/province |
Bavaria |
| ZIP/Postal code |
93053 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11532 |
| Series (1) |
| GSE51305 |
Gene expression profiles of Sunitinib-treated but not untreated short-term serum-free cultures predict treatment response of human high-grade gliomas in vitro |
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