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Sample GSM995703 Query DataSets for GSM995703
Status Public on Dec 10, 2012
Title Skeletal muscle from obese male 8, control
Sample type RNA
 
Channel 1
Source name mix of liver, adipose tissue and skeletal muscle
Organism Homo sapiens
Characteristics gender: mix of male and female
tissue: mix of liver, adipose tissue and skeletal muscle
Biomaterial provider mix of liver, adipose tissue and skeletal muscle
Extracted molecule total RNA
Extraction protocol Total RNA was purchased at Applied Biosystems/Ambion
Label Cy3
Label protocol Total RNA quality was checked by capillary electrophoresis (Experion, BioRad) and quantified using Nanodrop ND-1000 Spectrophotometer (Labtech). Only good quality RNA extracts only were used for microarray hybridization. Fluorescent probes were obtained by amplifying and labelling 200ng of RNA with the low RNA input linear amplification kit (Agilent).
 
Channel 2
Source name Human vastus lateralis muscle, control (before training)
Organism Homo sapiens
Characteristics treatment: before training
gender: male
tissue: skeletal muscle
Extracted molecule total RNA
Extraction protocol Tissue was crushed in QIAzol (Qiagen) and total RNA was extracted with the RNeasy mini kit (Qiagen) according to manufacturer instructions.
Label Cy5
Label protocol Total RNA quality was checked by capillary electrophoresis (Experion, BioRad) and quantified using Nanodrop ND-1000 Spectrophotometer (Labtech). Only good quality RNA extracts only were used for microarray hybridization. Fluorescent probes were obtained by amplifying and labelling 200ng of RNA with the low RNA input linear amplification kit (Agilent).
 
 
Hybridization protocol 825 ng of Cy5 labelled probe was cohybridized the same amount of Cy3 labelled control probe. We used the Whole Human Genome Microarray Kit, 4x44K from Agilent with the gene expression hybridization kit according to the manufacturer’s protocol.
Scan protocol Micro-arrays were scanned on a InnoScan 710A scanner (Innopsys, Carbonne, France, EU) and data were extracted with Mapix software version 5.5.0 (Innopsys).
Description Labeling and hybridization qualities were verified with Agilent’s spike in kit.
Data processing Features with a signal to background ratio strictly below 2 in both color as well as control spots were discarded. The data without background subtraction were normalized with the Lowess procedure and quantiles method by use of R. Value is the Log2 of normalized 635/ 532 value ratio.
 
Submission date Aug 31, 2012
Last update date Dec 10, 2012
Contact name Nathalie Viguerie
Organization name INSERM
Department I2MC U1297
Lab MetaDiab
Street address Avenue Poulhes
City Toulouse
ZIP/Postal code 31400
Country France
 
Platform ID GPL16022
Series (1)
GSE40551 Effects of a 8-week training on human skeletal muscle

Data table header descriptions
ID_REF
VALUE log2 ratio of trained skeletal muscle vs reference pool

Data table
ID_REF VALUE
ZBTB10
THC2669500
TSG101 0.689741679
SPG3A
SFXN3
SNX15
MTHFR
C11orf2 -0.010744107
ADORA3
A_24_P928815
CTAGEP
ETS1
FLJ38377
TERF2
AF090926
CACNA2D3 1.350510496
KIAA1909
GRM4
GHRL
FBXW2

Total number of rows: 30499

Table truncated, full table size 397 Kbytes.




Supplementary file Size Download File type/resource
GSM995703_CG008_V2_A_251485064758_05.gpr.gz 11.2 Mb (ftp)(http) GPR
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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