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Sample GSM1092488 Query DataSets for GSM1092488
Status Public on Mar 05, 2013
Title GBM_differentiation_4days_4
Sample type RNA
 
Source name Glioblastoma multiforme cells, differentiation, 4 days
Organism Homo sapiens
Characteristics tissue: Brain
disease status: Glioblastoma multiforme
patient: G63
cell type: differentiated 4 days
Treatment protocol Glioblastoma neurospheres were differentiated in the presence of 10% fetal calf serum and in absence of B-27 supplement for 4days
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 The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
Label Biotin
Label protocol The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).
 
Hybridization protocol Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133A 2.0 chip according to the protocols provided by the manufacturer.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
Description reanalysis of GSM520525
Data processing Data analysis performed using R (2.15.0) and Bioconductor packages. The function rma of package affy (1.36.0) was used for normalization
 
Submission date Mar 04, 2013
Last update date Mar 05, 2013
Contact name Raquel Malumbres
E-mail(s) rmalumbres@yahoo.com
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 GPL570
Series (2)
GSE44841 Microarray analysis of differentiation of human glioblastoma neurospheres
GSE44843 Involvement of miRNAs in the Differentiation of Human Glioblastoma Multiforme Brain Tumor Stem-Like Cells
Relations
Reanalysis of GSM520525

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 11.04683608
1053_at 10.06845508
117_at 5.962377666
121_at 7.971309615
1255_g_at 3.202917965
1294_at 7.934700546
1316_at 4.85730308
1320_at 5.446508479
1405_i_at 3.039203128
1431_at 4.462328881
1438_at 8.386001693
1487_at 8.593367709
1494_f_at 5.990737999
1552256_a_at 10.82172256
1552257_a_at 9.885387691
1552258_at 7.231679427
1552261_at 4.769872115
1552263_at 6.392115725
1552264_a_at 8.12803021
1552266_at 5.22774216

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1092488_G63_DF_4d_12209.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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