|
| Status |
Public on Mar 05, 2013 |
| Title |
G59_NS |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
GBM neurospheres derived from a tumor sample of G59 patient
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: GBM neurospheres derived from a tumor sample of G59 patient
|
| Treatment protocol |
Glioblastoma neurospheres were differentiated in the presence of 10% fetal calf serum and in absence of B-27 supplement for 4 and 14 days
|
| Growth protocol |
Tumor cells were resuspended in serum-free DMEM/F12 medium (Invitrogen, Carlsbad, CA) containing human recombinant EGF (20 ng/ml; Sigma, St. Louis, MO), bFGF (20 ng/ml; Sigma), B-27 (20 ml per ml of medium; Invitrogen) and heparin (2 mg/ml), and seeded at a density of 3x106 live cells/60-mm plate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the GBM cell lines G52, G63, G59, GN1C and G97C, at the neurosphere state or after 4 or 14 days of differentiation, was extracted using mirVana miRNA Isolation Kit (Ambion) and analyzed with the 2100 Bioanalyzer (Agilent). All of the samples showed a RIN value of ≥ 8.0.
|
| Label |
Hy3
|
| Label protocol |
1000 ng of total RNA were labeled with miRCURY Hy3/Hy5 Power labeling kit (Exiqon) . Each individual sample was labeled with Hy3 and the common reference pool of all samples with Hy5.
|
| |
|
| Channel 2 |
| Source name |
common reference: a pool of all samples
|
| Organism |
Homo sapiens |
| Characteristics |
reference: pool of all samples
|
| Treatment protocol |
Glioblastoma neurospheres were differentiated in the presence of 10% fetal calf serum and in absence of B-27 supplement for 4 and 14 days
|
| Growth protocol |
Tumor cells were resuspended in serum-free DMEM/F12 medium (Invitrogen, Carlsbad, CA) containing human recombinant EGF (20 ng/ml; Sigma, St. Louis, MO), bFGF (20 ng/ml; Sigma), B-27 (20 ml per ml of medium; Invitrogen) and heparin (2 mg/ml), and seeded at a density of 3x106 live cells/60-mm plate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the GBM cell lines G52, G63, G59, GN1C and G97C, at the neurosphere state or after 4 or 14 days of differentiation, was extracted using mirVana miRNA Isolation Kit (Ambion) and analyzed with the 2100 Bioanalyzer (Agilent). All of the samples showed a RIN value of ≥ 8.0.
|
| Label |
Hy5
|
| Label protocol |
1000 ng of total RNA were labeled with miRCURY Hy3/Hy5 Power labeling kit (Exiqon) . Each individual sample was labeled with Hy3 and the common reference pool of all samples with Hy5.
|
| |
|
| |
| Hybridization protocol |
The hybridization was performed according to the miRCURY LNA™ microRNA Array instruction manual using a Tecan HS 4800™ hybridization station (Tecan, Austria). Samples were hybridized onto miRNA miRCURY™ LNA Array version 5th Generation (Exiqon)
|
| Scan protocol |
The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).
|
| Data processing |
The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al.) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm after removal of empty spots and controls
|
| |
|
| Submission date |
Mar 04, 2013 |
| Last update date |
Mar 05, 2013 |
| Contact name |
Raquel Malumbres |
| E-mail(s) |
[email protected]
|
| Phone |
+34 948194700
|
| Organization name |
University of Navarra/ Clínica Universidad de Navarra
|
| Department |
Hemato-Oncology
|
| Lab |
Multiple Myeloma
|
| Street address |
Avenida Pio XII 55
|
| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11432 |
| Series (2) |
| GSE44842 |
Involvement of miRNAs in the induced differentiation of glioblastoma multiforme brain tumor stem-like cells [Exiqon miRNA array] |
| GSE44843 |
Involvement of miRNAs in the Differentiation of Human Glioblastoma Multiforme Brain Tumor Stem-Like Cells |
|
