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Sample GSM1275714 Query DataSets for GSM1275714
Status Public on Oct 13, 2014
Title Mdx skeletal muscle, PBS+running for 7 weeks rep 3
Sample type RNA
 
Source name Mdx skeletal muscle_PBS+running for 7 wks
Organism Mus musculus
Characteristics strain: Mdx
gender: male
age: 6-7 weeks
sample group: PBS+running for 7 weeks
tissue: gastrocnemius muscle
Extracted molecule total RNA
Extraction protocol Gastrocnemius muscle was pulverized and homogenized in liquid nitrogen and exactly 70 mg of muscle powder was weighted into Trizol reagent (Invitrogen, Carlsbad, CA, USA). Total RNA and DNA fractions were extracted according to the manufacturer’s guidelines. The RNA and DNA concentrations were analyzed with Nanodrop ND-1000 (Thermo Fisher Scientific Inc., Waltham MA, USA) in duplicate. The quality of RNA was confirmed by spectrophotometry (OD260/OD280 ratio of 1.9 to 2.0) and agarose gel electrophoresis. Possible DNA still left was further degraded using DNAse according to the manufacturer’s instructions (TURBO DNA-free™ Kit, Applied Biosystems by Life Technologies, USA).
Label biotin
Label protocol Biotinylated cRNA were prepared with Illumina TotalPrep RNA Amplification Kit (Applied Biosystems cat # AMIL1791).
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description SAMPLE 3
Data processing The data were normalized with quantiles normalization (including log2-transformation of the data) and data quality was assessed using Chipster software (IT Center for Science, Espoo, Finland)
 
Submission date Nov 26, 2013
Last update date Oct 13, 2014
Contact name Juha J Hulmi
E-mail(s) juha.hulmi@jyu.fi
Organization name University of Jyväskylä
Department Biology of Physical Activity
Street address Rautpohjankatu 8a Viv
City Jyväskylä
ZIP/Postal code 40014
Country Finland
 
Platform ID GPL6885
Series (1)
GSE52766 The effects of muscular dystrophy, exercise and sActRIIB-Fc on molecular signature of skeletal muscle in mice

Data table header descriptions
ID_REF
VALUE quantile normalized with Chipster software
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 12.25 0
ILMN_2721178 10.68 0
ILMN_3033922 9.94 0
ILMN_3092673 11.92 0
ILMN_2816356 6.54 0.04385965
ILMN_2808939 7.86 0
ILMN_2634564 9.41 0
ILMN_2737647 6.36 0.1428571
ILMN_2734484 8.49 0
ILMN_2952292 6.71 0.01503759
ILMN_2699078 6.1 0.4598998
ILMN_1213681 9.13 0
ILMN_2735413 6.04 0.5964912
ILMN_2735415 6.47 0.07393484
ILMN_2891688 9.36 0
ILMN_2637698 9.18 0
ILMN_2674228 8.38 0
ILMN_2601546 6.26 0.2205514
ILMN_1230831 6.31 0.1704261
ILMN_2848071 6.38 0.1303258

Total number of rows: 25697

Table truncated, full table size 636 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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