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Sample GSM694205 Query DataSets for GSM694205
Status Public on Sep 15, 2011
Title Dorsocervical vs. abdominal subcutaenous adipose tissue U32
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

Data table header descriptions
ID_REF
VALUE log2 ratio (Cy5/Cy3) abdominal subcutaneous/dorsocervical adipose

Data table
ID_REF VALUE
1 0.579181287
2 0.7014276
3
4
5 -0.029618812
6
7
8
9
10 2.153959956
11
12
13
14
15
16
17
18
19 3.213223492
20 0.386355534

Total number of rows: 45220

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM694205.gpr.gz 10.3 Mb (ftp)(http) GPR
Processed data included within Sample table

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