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Status |
Public on Dec 10, 2012 |
Title |
Skeletal muscle from obese male 18 after 8-week training |
Sample type |
RNA |
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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 |
tissue: 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).
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Channel 2 |
Source name |
Human vastus lateralis muscle, trained (after training)
|
Organism |
Homo sapiens |
Characteristics |
treatment: after 8-week 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).
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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.
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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).
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Description |
Labeling and hybridization qualities were verified with Agilent’s spike in kit.
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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.
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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 |
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Platform ID |
GPL16022 |
Series (1) |
GSE40551 |
Effects of a 8-week training on human skeletal muscle |
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