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Sample GSM1370579 Query DataSets for GSM1370579
Status Public on Jul 07, 2014
Title Wnt3a treated DRG culture rep2
Sample type RNA
 
Source name mouse DRG tissue
Organism Mus musculus
Characteristics strain: C57Bl/6
age: 4-6 weeks
tissue: neuronal-enriched DRG culture
treatment: Wnt3a
Treatment protocol The DRG cultures were serum-starved for 1h and then treated with Wnt3a (200 ng/ml) or vehicle (PBS) for 6h.
Growth protocol DRGs from 6-8 weeks old mice were collected in cold PBS after removing axons and meningeal tissue, and digested for 30 min at 37°C in trypsin, collagenase and DNAse. Neurons were than separated from non-neuronal cells using a discontinuous Percoll gradient, plated on poly-L-lysine coated coverslips and cultured in F12 medium plus 10% serum in presence of a mixture of growth factors (BDNF 10 ng/ml, NGF 10 ng/ml, GDNF 5 ng/ml, NT3 5ng/ml, all from SIGMA) and mitotic inhibitor AraC 5 µM (SIGMA) for 3 days before treatment.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol (Life Technologies) followed by clean-up and DNase I treatment with Qiagen RNeasy mini kit in accordance with the prescribed protocol provided with the kit. RNA quality control was performed with Agilent Bioanalyzer.
Label biotin
Label protocol Biotinylated cRNA was prepared with the Ambion TotalPrep kit for Illumina arrays.
 
Hybridization protocol Microarrays were hybridized following Illumina's standard hybridization protocol on MouseRef-8 v2.0 expression BeadChips.
Scan protocol Processed arrays were scanned on Illumina iScan System array reader according to the manufacturer's instructions.
Description replicate 2
Data processing Raw array data were processed with Illumina BeadStudio software (v3.2) using background subtraction and cubic-spline normalisation.
 
Submission date Apr 17, 2014
Last update date Jul 07, 2014
Contact name Emil Karaulanov
E-mail(s) e.karaulanov@imb-mainz.de
Organization name Institute of Molecular Biology
Street address Ackermannweg 4
City Mainz
ZIP/Postal code 55128
Country Germany
 
Platform ID GPL6885
Series (1)
GSE56880 Genome-wide transcriptome analysis of neuron-enriched DRG cultures exposed to Wnt3a

Data table header descriptions
ID_REF
VALUE background subtracted and cubic spline normalised signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 -3.800113 0.679198
ILMN_1212612 698.981 0
ILMN_1212619 120.3605 0
ILMN_1212628 15.60367 0.04135338
ILMN_1212632 23.28954 0.005012531
ILMN_1212636 2510.496 0
ILMN_1212637 107.3166 0
ILMN_1212645 -26.11955 0.9837093
ILMN_1212648 100.7376 0
ILMN_1212653 51.95818 0
ILMN_1212672 35.24841 0.001253133
ILMN_1212682 -25.83673 0.981203
ILMN_1212683 -12.10968 0.9010025
ILMN_1212685 -2.136274 0.6015037
ILMN_1212692 20.29734 0.01253133
ILMN_1212693 10.12774 0.1278196
ILMN_1212695 7.622597 0.1992481
ILMN_1212698 -11.40197 0.8897243
ILMN_1212702 94.76736 0
ILMN_1212703 11.79163 0.09774436

Total number of rows: 25697

Table truncated, full table size 737 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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