|
|
| Status |
Public on Mar 20, 2015 |
| Title |
U87 |
| Sample type |
RNA |
| |
|
| Source name |
Glioblastoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Glioblastoma cell line
tissue: Brain
stem cell: No
|
| Growth protocol |
GSCs were cultured in DMEM/F12 (Invitrogen) supplemented with B27 (1:50), heparin (5 mg/mL), basic FGF (bFGF) (20 ng/mL), and EGF (20 ng/mL). LN428 cells were cultured in alpha MEM supplemented with 10% heat inactivated FBS, L-glutamine antibiotic/antimycotic and gentamycin. T98G and U87 glioblastoma cells were cultured in EMEM supplemented with 10% heat inactivated FBS,Sodium Pyruvate,MEM Non Essential Amino acids, antibiotic/antimycotic and Gentamycin. U373 glioblastoma cells were cultured DMEM containing 10% heat inactivated FBS, 100 units/mL penicillin, and 100 μg/mL streptomycin. LN444 and LN44-AA cells were cultured in DMEM with high glucose (Invitrogen) containing 10% (vol/vol) FBS (HyClone-Thermo Fisher), 100 units/mL penicillin, and 100 μg/mL streptomycin (Invitrogen). All the cells were maintained in a humidified 5% CO2 incubator at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected in the exponential phase of growth by 500 rpm centrifigation and then washed twice with 1x PBS. Followed, the cells were lysed with 1 mL Qiazol lysis reagent.Total RNA was then extracted and purified using the Qiagen RNeasy Mini kit (catalog no. 217004) according to the manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated antisense RNA were prepared according to the standard Affymetrix protocol from 100ng total RNA using an GeneCHip 3′ IVT Express kit (Affymetrix), as described by the manufacturer.
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| |
|
| Hybridization protocol |
The labeled aRNAs were then mixed with hybridization master mix, and the hybridization mixtures were then denatured at 95 °C for 5 min, followed by 45 °C for 5 min, and then kept at 45 °C until applied to the hybridization tray (GeneAtlas System; 120 μL hybridization mixture of a cell culture was transferred into a well of a four-well hybridization tray). The array strip was immerse into hybridization mixture and incubated in theHybridization Station at 45 °C for 16 h.
|
| Scan protocol |
The intensity of each hybridized probe was generated using the GeneAtlas Imaging Station.
|
| Description |
Gene expression data from a Glioblastoma cell line
|
| Data processing |
The raw .CEL files were normalized and summarized using RMA method in R Bioconductor.
|
| |
|
| Submission date |
Mar 19, 2015 |
| Last update date |
Mar 20, 2015 |
| Contact name |
Uma Chandran |
| E-mail(s) |
chandran@pitt.edu
|
| Phone |
412-648-9326
|
| Organization name |
University of Pittsburgh
|
| Department |
BioMedical Informatics
|
| Street address |
5150 Center Ave
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15232 |
| Country |
USA |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
| GSE67089 |
Analysis of mRNA profiles distinguishes proneural (PN) glioma stem cells (GSC) from mesenchymal (Mes) GSCs |
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