|
| Status |
Public on Sep 15, 2011 |
| Title |
Dorsocervical vs. abdominal subcutaenous adipose tissue U28 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Dorsocervical adipose tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Dorsocervical adipose tissue
disease state: HIV+
treatment result: developed lipodystrophy
|
| Treatment protocol |
Adipose tissue was homogenised using the Geneclean kit (Bio101 systems, Obiogene Inc., Carlsbad, CA). RNA was extracted with the RNeasy Lipid Tissue Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Quantity and integrity of RNA were verified using RNA 6000 nanochips (Agilent 2100 Bioanalyser, Palo Alto, CA). Part of the isolated RNA was stored at -80°C until quantification of the target mRNAs by microarray.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The amplified RNA (aRNA, 5 µg/sample) was labelled using monoreactive Cy3 or Cy5 dyes (GE Healthcare, GE Life Sciences, Uppsala, Sweden) followed by purification according the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Labelled aRNAs was hybridized onto Whole Human Genome 4x44K microarrays (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s instructions. The slides were then washed according to the instructions with buffers from Agilent.
|
| |
|
| Channel 2 |
| Source name |
Abdominal subcutaneous adipose tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Abdominal subcutaneous adipose tissue
disease state: HIV+
treatment result: developed lipodystrophy
|
| Treatment protocol |
Adipose tissue was homogenised using the Geneclean kit (Bio101 systems, Obiogene Inc., Carlsbad, CA). RNA was extracted with the RNeasy Lipid Tissue Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Quantity and integrity of RNA were verified using RNA 6000 nanochips (Agilent 2100 Bioanalyser, Palo Alto, CA). Part of the isolated RNA was stored at -80°C until quantification of the target mRNAs by microarray.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The amplified RNA (aRNA, 5 µg/sample) was labelled using monoreactive Cy3 or Cy5 dyes (GE Healthcare, GE Life Sciences, Uppsala, Sweden) followed by purification according the manufacturer’s instructions.
|
| Label |
Cy5
|
| Label protocol |
Labelled aRNAs was hybridized onto Whole Human Genome 4x44K microarrays (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s instructions. The slides were then washed according to the instructions with buffers from Agilent.
|
| |
|
| |
| Hybridization protocol |
The slides were scanned with GenePix 4200 AL (Axon Instruments, Molecular Devices, Silicon Valley, CA) at the resolution of 5 µm/pixel and at 16 bit depth.
|
| Scan protocol |
GPR files were imported in R v. 2.10 and preprocessed by the BioConductor package limma.
|
| Description |
Lipodystrophic patient
|
| Data processing |
quantile normalized log ratios (base2) from the median foregraound intensities with no background correction.
|
| |
|
| Submission date |
Mar 21, 2011 |
| Last update date |
Sep 15, 2011 |
| Contact name |
Dario Greco |
| E-mail(s) |
dario.greco@tuni.fi
|
| Organization name |
Tampere University
|
| Department |
Faculty of Medicine and Health Technology
|
| Lab |
Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)
|
| Street address |
Arvo ylpön Katu 34
|
| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE28073 |
COMPARISON OF DORSOCERVICAL TO ABDOMINAL SUBCUTANEOUS ADIPOSE TISSUE IN PATIENTS WITH AND WITHOUT ANTIRETROVIRAL THERAPY-ASSOCIATED LIPODYSTROPHY |
|
