|
| Status |
Public on Apr 03, 2009 |
| Title |
Patient 5 Subcutaneous Lean |
| Sample type |
RNA |
| |
|
| Source name |
adipose tissue
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 5
tissue: Subcutaneous adipose tissue
surgery: Hernia surgery
age: 64 years
gender: Male
body mass index: 27.4 BMI
body size category: lean
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Adipose tissue was collected at the beginning of the operation (within 30 minutes) into sterile 50 mL conical tubes and immediately flash- frozen in liquid nitrogen. Subcutaneous adipose tissue was collected from the subcutaneous abdominal wall and omental adipose tissue was collected from the greater omentum which is representative of intra-abdominal adipose depots drained by the portal vein. RNA was extracted from tissues using Qiagen spin columns (Qiagen, Mississauga, Canada) following manufacturer’s protocol for fatty tissue with the addition of two RNase free DNase treatments (Qiagen) between RW1 washes. RNA quality was assessed by spectrometry (260/280 ratio) with ratios of 1.9 – 2.0. As well, RNA quality was assessed by chromatography.
|
| Label |
Biotin labelled cRNA
|
| Label protocol |
cRNA was synthesized by in vitro transcription and hybridisation as previously described. Briefly, 10 ug of high quality total RNA was converted to cDNA and then to biotin-labelled cRNA (10 mM Biotin-11-UTP, Perkin-Elmer) by linear amplification (iExpress Assay reagent kit, GE Healthcare Bio-Sciences, Montreal, Quebec).
|
| |
|
| Hybridization protocol |
10 ug of labelled cRNA was hybridised to CodeLink UniSet Human 20K I (GE Healthcare Bio-Sciences).
|
| Scan protocol |
The microarray slides were processed according to manufacturer’s instructions and analysed using Codelink System Software (GE Healthcare Bio-Sciences).
|
| Description |
10 ug of labelled cRNA was hybridised to CodeLink UniSet Human 20K I (GE Healthcare Bio-Sciences). The microarray slides were processed according to manufacturer’s instructions and analysed using Codelink System Software (GE Healthcare Bio-Sciences). The spot intensities were median normalized (signal intensity of probe / median intensity of all discovery probes).
|
| Data processing |
The spot intensities were median normalized (signal intensity of probe / median intensity of all discovery probes).
|
| |
|
| Submission date |
Apr 02, 2009 |
| Last update date |
Apr 19, 2010 |
| Contact name |
Katherine Cianflone |
| E-mail(s) |
katherine.cianflone@crhl.ulaval.ca
|
| Organization name |
Laval University
|
| Street address |
2725 Ste Foy
|
| City |
Quebec |
| State/province |
Quebec |
| ZIP/Postal code |
G1V 4G5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL4044 |
| Series (1) |
| GSE15524 |
Individualized analysis of subcutaneous and omental abdominal adipose tissue from non-obese and obese subjects |
|
