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Sample GSM1092503 Query DataSets for GSM1092503
Status Public on Mar 05, 2013
Title G63_14d
Sample type RNA
 
Channel 1
Source name GBM neurospheres derived from a tumor sample of G63 patient upon 14 days of differentiation
Organism Homo sapiens
Characteristics cell type: GBM neurospheres derived from a tumor sample of G63 patient upon 14 days of differentiation
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

Data table header descriptions
ID_REF
VALUE Lowess normalized log2 median ratios representing test/reference (Hy3/Hy5)

Data table
ID_REF VALUE
42629 -3.869152104
42806 -3.177253174
46514 -4.063527264
5740 1.237289841
11091 -3.013993951
145642 -3.039588798
11052 0.795128171
11023 1.680735244
46711 -1.225109043
11005 -2.920049061
17885 -2.45512934
29490 -0.03716956
145914 -0.875194158
145832 -2.599112567
11022 1.68057798
11038 -2.184295883
17944 -1.899371156
17482 -1.74080426
46921 -2.501372594
11093 -1.56227946

Total number of rows: 1410

Table truncated, full table size 14 Kbytes.




Supplementary file Size Download File type/resource
GSM1092503_1_Exiqon_14223145_S01.txt.gz 889.1 Kb (ftp)(http) TXT
Processed data included within Sample table

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