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Sample GSM520523 Query DataSets for GSM520523
Status Public on Mar 01, 2011
Title GBM_differentiation_4 days_2
Sample type RNA
 
Source name glioblastoma stem cells, differentiation, 4 days
Organism Homo sapiens
Characteristics tissue: brain
disease status: glioblastoma
cell type: stem cells G52
Treatment protocol glioblastoma stem cells were differentiated in the presence of FCS for 4 days
Growth protocol Tumor cells were then 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 plated 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 G52_DF_4d.CEL
Data processing Data analysis performed using R (2.8.1) and Bioconductor packages. The function rma of package affy (1.20.2) was used for normalization.
 
Submission date Mar 10, 2010
Last update date Mar 04, 2013
Contact name Victor Segura
E-mail(s) vsegura@unav.es
Organization name FIMA
Department Unit of Proteomics, Genomics and Bioinformatics
Street address Avda. Pío XII, 55
City Pamplona
State/province Navarra
ZIP/Postal code 31008
Country Spain
 
Platform ID GPL570
Series (1)
GSE20736 Microarray analysis of differentiation of human glioblastoma stem cells
Relations
Reanalyzed by GSM1092484

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 11.25881118
1053_at 9.706865554
117_at 6.023976923
121_at 8.316482953
1255_g_at 3.115400528
1294_at 7.841210222
1316_at 5.231414759
1320_at 5.714706969
1405_i_at 3.212239714
1431_at 3.640799591
1438_at 6.417553272
1487_at 8.933461133
1494_f_at 6.028623867
1552256_a_at 9.304848167
1552257_a_at 9.33091893
1552258_at 6.397608857
1552261_at 4.521392455
1552263_at 7.821394628
1552264_a_at 8.893089127
1552266_at 4.552711996

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM520523.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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