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Sample GSM747392 Query DataSets for GSM747392
Status Public on Dec 22, 2011
Title N2a cells transfected by FLAG 5
Sample type RNA
Source name Neuroblastoma cells
Organism Mus musculus
Characteristics tissue: Brain
cell line: N2a neuroblastoma cells
genotype/variation: control
Treatment protocol Cells were transfected with an expression vector expressing Arx using Lipofectamine 2000 according to the guideline of the manufacturer (Invitrogen)
Growth protocol N2a cells were grown in Dulbecco's Modified Eagle Medium (DMEM) high glucose (PAA) which was supplemented with 10% fetal bovine serum gold (PAA), 2 mM L-glutamine (Lonza), 0,1 mM non essential amino-acids (Gibco) and 2 mM penicillin/streptomycin (PAA). Cells were grown at 37°C with 5% CO2.
Extracted molecule total RNA
Extraction protocol Two days after transfection, RNA from N2a cells was isolated using the Total RNA Isolation Nucleospin RNA II kit following the manufacturer's instructions (Macherey-Nagel).
Label Cy5
Label protocol RNA was labelled using the Low Input Quick Amp Labelling kit (Agilent Technologies). The fluorescent labelled cRNA probes were purified using the RNeasy Mini kit (Qiagen).
Hybridization protocol 825 ng of cyanine-labeled, linearly amplified cRNA were hybridized at 65°C at 10 rpm for 17 hours, with 10X Blocking Agent, 25X Fragmentation Buffer, Nuclease free water and 2X GEx Hybridization Buffer HI-RPM (Agilent Technologies). Samples were hybridized on Mouse Gene Expression 4x44K V2 microarray (Agilent Technologies).
Scan protocol Hybridization images were obtained using an Agilent DNA microarray scanner (G2505B). Profile : Agilent HD_GX_2color / Scan Region : Agilent HD (61 x 21,6 mm) / Resolution : 5 µm / TIFF : 20 bit / RPMT : 100% / GPMT : 100%. Intensity data were extracted using Feature Extraction software (FE v9,5,1) (Agilent Technologies).
Description FLAG-5_10142_1
Data processing The Lowess method was used to normalize data expression (using in-house R script).
Submission date Jun 24, 2011
Last update date Dec 22, 2011
Contact name Gaelle Friocourt
Phone +33 298443895
Fax +33 298467910
Organization name Inserm U613
Department Molecular Genetics
Street address 46 rue Félix Le Dantec, CS51819
City Brest
ZIP/Postal code 29218
Country France
Platform ID GPL10333
Series (2)
GSE30190 Comparison of gene expression between Arx-transfected N2a cells and cells transfected by the corresponding empty vector
GSE30191 ARX transcription factor implicated in mental retardation and epilepsy

Data table header descriptions
VALUE Lowess normalized signal

Data table
1 12608
2 44.5
3 40.5
4 42
5 42
6 44
7 40
8 45
9 47.5
10 46
11 44
12 1268
13 72
14 67.5
15 259
16 4110.5
17 17505.5
18 75
19 67
20 110.5

Total number of rows: 44397

Table truncated, full table size 448 Kbytes.

Supplementary file Size Download File type/resource
GSM747392_US45103054_252665510142_S01_GE2_107_Sep09_1_1.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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