|
| Status |
Public on Jan 23, 2017 |
| Title |
U3027 cell line |
| Sample type |
RNA |
| |
|
| Source name |
Primary human GBM
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Glioma stem cells
|
| Treatment protocol |
No treatment
|
| Growth protocol |
The cells were cultured in DMEM/F12 Glutamax (Gibco) and Neurobasal medium (Gibco) mixed 1:1 with addition of 1% B27 (Invitrogen), 0.5% N2 (Invitrogen), 1% Penicillin/Streptomycin (Sigma), 10 ng/ml each of EGF and FGF2 (Peprotech) on poly-ornithine/laminin-coated dishes as adherent cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was extracted using the QIAGEN RNeasy kit (QIAGEN)
|
| Label |
biotin
|
| Label protocol |
250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual (P/N 703174 Rev 1 Affymetrix Inc., Santa Clara, CA).
|
| |
|
| Hybridization protocol |
GeneChip® ST Arrays (GeneChip® Human Transcriptome Array 2.0) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA) the arrays were washed and stained using the Fluidics Station 450.
|
| Scan protocol |
The arrays were scanned using the GeneChip® Scanner 3000 7G.
|
| Description |
Surgical tissue samples and clinical information were obtained from treatment naive patients subjected to brain tumor removal
|
| Data processing |
The raw data was normalized in the free software Expression Console provided by Affymetrix (http://www.affymetrix.com) using the robust multi-array average (RMA) method first suggested by Li and Wong (PNAS, 2001). Only probesets annotated as being in category main were included in further analyses.
|
| |
|
| Submission date |
Dec 09, 2016 |
| Last update date |
Jan 23, 2017 |
| Contact name |
Sven Nelander |
| Organization name |
Uppsala University
|
| Department |
Department of Immunology, Genetics and Pathology
|
| Lab |
Rudbeck Laboratory
|
| Street address |
Dag Hammarskjölds v. 20
|
| City |
Uppsala |
| ZIP/Postal code |
75185 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17586 |
| Series (2) |
| GSE91392 |
Human expression data from Glioblastoma cell malignancy and drug sensitivity are affected by the cell of origin. |
| GSE91393 |
Glioblastoma cell malignancy and drug sensitivity are affected by the cell of origin |
|
