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Sample GSM1245003 Query DataSets for GSM1245003
Status Public on Nov 07, 2015
Title NNI-1 [4310479108_D]
Sample type RNA
 
Source name Primary neurosphere
Organism Homo sapiens
Characteristics pna: PNA.hi
histology: GBM
grade: IV
replicate: D
Growth protocol Graded brain tumor specimens were obtained with informed consent, as part of a study protocol approved by the SingHealth Centralised Institutional Review Board A. GPC lines were described in our previous work. Briefly, cells were seeded as free-floating spheres at a density of 2,500 cells per cm2 in chemically defined serum-free growth medium containing basic fibroblast growth factor (bFGF; 20 ng/ml; PeproTech, New Jersey), epidermal growth factor (EGF; 20 ng/ml; PeproTech), heparin (5 μg/ml; Sigma-Aldrich, St Louis), and serumfree supplement (B27; 1x; Gibco, Grand Island, NY) in a 3:1 mix of Dulbecco’s modified Eagle’s medium (DMEM; Sigma-Aldrich) and Ham’s F-12 Nutrient Mixture (F-12; Gibco). Neurospheres were mechanically triturated with a flame-drawn glass Pasteur pipette twice weekly and re-seeded in fresh culture medium
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tumor neurospheres using TRI Reagent (Molecular Research Center, Cincinnati, OH). Thereafter, RNA samples were hybridized to Illumina HumanRef-8 v2 Expression Beadchip Array.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina HumanRef-8 v2 Expression Beadchip
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Data processing The data were normalised using quantile normalisation on exonic probesets with lumi packages in R
 
Submission date Oct 18, 2013
Last update date Nov 07, 2015
Contact name Edwin Sandanaraj
Phone 6564070112
Organization name NNI
Department Research
Lab Neuro-Oncology
Street address 11 Jalan Tan Tock Seng
City Singapore
ZIP/Postal code Singapore
Country Singapore
 
Platform ID GPL14186
Series (2)
GSE51411 ST3GAL1-Associated Transcriptomic Program in Glioblastoma Tumor Growth, Invasion, and Prognosis
GSE51413 ST3GAL1-Associated Transcriptomic Program in Glioblastoma Tumor Growth, Invasion, and Prognosis

Data table header descriptions
ID_REF
VALUE quantile normalized
Detection.4310479108_D

Data table
ID_REF VALUE Detection.4310479108_D
ILMN_1762337 7.062063112 0.02684
ILMN_1779670 7.169373504 0.54237
ILMN_1806310 7.153943813 0.44492
ILMN_1671474 7.247646144 0.88559
ILMN_1731507 7.134560743 0.30932
ILMN_1814316 7.187162266 0.64689
ILMN_1745607 11.28219805 1
ILMN_1757454 7.202875975 0.7274
ILMN_1735045 7.254890374 0.89548
ILMN_1680754 7.21873783 0.78531
ILMN_1755321 8.040016514 1
ILMN_1698554 8.326970354 1
ILMN_1805938 7.109413576 0.16808
ILMN_1676336 7.66747021 0.99718
ILMN_1752884 7.115056894 0.19492
ILMN_1668851 7.247646144 0.88559
ILMN_1809959 7.189741721 0.66102
ILMN_1801812 7.253889386 0.89407
ILMN_1726986 8.775656791 1
ILMN_1689211 7.156403108 0.45621

Total number of rows: 18270

Table truncated, full table size 548 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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