|
| Status |
Public on Dec 07, 2010 |
| Title |
Subcutaneous Adipose tissue_Lean_2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Reference RNA pool made of a mix of commercial human liver, adipose tissue and skeletal muscle
|
| Organism |
Homo sapiens |
| Characteristics |
agent: none
gender: mix of male and female
tissue: mix of liver, adipose tissue and skeletal muscle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy Mini kit (Qiagen) according to manufacturer instructions.
|
| Label |
Cy3
|
| Label protocol |
RNA quantity and quality were checked with the Experion automated electrophoresis system (BioRad Laboratories).
Total RNA (250 ng) from each sample was amplified and transcribed into fluorescent cRNA using Low RNA Input Linear Amplification kit (Agilent Technologies).
|
| |
|
| Channel 2 |
| Source name |
Human subcutaneous adipose tissue, lean
|
| Organism |
Homo sapiens |
| Characteristics |
agent: lean
gender: female
tissue: subcutaneous adipose tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy Mini kit (Qiagen) according to manufacturer instructions.
|
| Label |
Cy5
|
| Label protocol |
RNA quantity and quality were checked with the Experion automated electrophoresis system (BioRad Laboratories).
Total RNA (250 ng) from each sample was amplified and transcribed into fluorescent cRNA using Low RNA Input Linear Amplification kit (Agilent Technologies).
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized to Agilent 44k whole human genome microarrays.
Sample preparation and microarray washing were performed according to manufacturer’s recommendations (Agilent Technologies).
|
| Scan protocol |
Arrays were scanned using InnoScan®700 scanner (Innopsys, Carbonne, France, EU).
Images were quantified using MAPIX®V3.02 software (Innopsys).
|
| Description |
Labelling and hybridization qualities were verified with Agilent's spike in kit
|
| Data processing |
Intensity ratios between Cy5 and Cy3 were filtered using an average intensity of 1.5 times above the background signal and normalized with a global Loess procedure without background substraction with R package LIMMA (Bioconductor).
Value is the Log2 of normalized Cy5/Cy3 value ratio.
|
| |
|
| Submission date |
Oct 21, 2010 |
| Last update date |
Dec 07, 2010 |
| 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 |
GPL4133 |
| Series (1) |
| GSE24883 |
Worsening of Obesity and Metabolic Status Yields Similar Molecular Adaptations_Subcutaneous and Visceral Adipose Tissue |
|
