NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1092493 Query DataSets for GSM1092493
Status Public on Mar 05, 2013
Title G97C_4d
Sample type RNA
 
Channel 1
Source name GBM neurospheres derived from a tumor sample of G97C patient upon 4 days of differentiation
Organism Homo sapiens
Characteristics cell type: GBM neurospheres derived from a tumor sample of G97C patient upon 4 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) 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 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 -0.145044841
42806 1.726879134
46514 0.647075685
5740 -2.884042559
11091 0.022962249
145642 -0.420726431
11052 -3.301724393
11023 -1.747976606
46711 -2.541369942
11005 0.080875784
17885 1.354951308
29490 -1.410576957
145914 0.396090147
145832 -0.036648463
11022 -1.306799881
11038 -0.361773492
17944 -0.076327336
17482 0.197143477
46921 0.374682077
11093 0.4403961

Total number of rows: 1410

Table truncated, full table size 13 Kbytes.




Supplementary file Size Download File type/resource
GSM1092493_1_Exiqon_14223134_S01.txt.gz 892.8 Kb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap