|
| Status |
Public on Jan 01, 2012 |
| Title |
Patient 1_Sub C_Day 0 |
| Sample type |
RNA |
| |
|
| Source name |
Patient 1_Sub C_Day 0
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
tissue: sub cutaneous adipose tissue
time post vbg: Day 0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the adipose tissue tissue using an RNeasy Lipid tissue mini kit followed by incubation with RNase free DNase (Qiagen, Crawley, West Sussex) for DNA-free RNA following the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
2 μg of high quality total RNA, verified using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies), was used with the Affymetrix Eukaryotic One-Cylce Target Labeling and Control reagents (#900493) following the manufacturers instructions to generate Biotin-labeled antisense cRNA.
|
| |
|
| Hybridization protocol |
The labeled and fragmented cRNA (10mg) was used for the hybridization to the Affymetrix (Santa Clara, CA) gene chips HS 1a520180 for 16 hr at 45C. An automated process of washing and staining in the Affymetrix Fluidics Station 400 was performed.
|
| Scan protocol |
Affymetrix arrays were scanned using the Affymetrix 3000G scanner. Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v1 software.
|
| Description |
080111MJA_Hs1a520180_NHo01
|
| Data processing |
CEL files were transferred to MadMax website (https://madmax.bioinformatics.nl), and data analysis was performed using the statistical programming language R and the R libraries offered by the Bioconductor project. The data were first explored for quality control purposes and were normalized the GCRMA method within Bioconductor.
|
| |
|
| Submission date |
May 20, 2011 |
| Last update date |
Jan 01, 2012 |
| Contact name |
Claus Mayer |
| E-mail(s) |
claus@bioss.ac.uk
|
| Organization name |
Biomathematics & Statistics Scotland
|
| Street address |
Greenburn Road
|
| City |
Aberdeen |
| ZIP/Postal code |
AB21 9SB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL7020 |
| Series (2) |
| GSE29409 |
Subcutaneous and omental white adipose tissue biopsies analysed from five obese patients |
| GSE29411 |
Expression data from human omental and subcutaneous adipose tissue taken from volunteers undergoing bariatric surgery |
|
