|
| Status |
Public on Jun 04, 2011 |
| Title |
subcutaneous fat_male_obese_rep4 |
| Sample type |
RNA |
| |
|
| Source name |
subcutaneous fat
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: subcutaneous adipose tissue
gender: male
weight: obese
array batch: 2
|
| Treatment protocol |
We collected fasting abdominal subcutaneous and, where possible, omental fat biopsies from otherwise healthy children having elective surgery at The Children’s Hospital at Westmead and the Institute of Weight Control, Baulkham Hills (Sydney, Australia). Participants were older than 6 months of age, lacked intercurrent illness (notably inflammatory disease) and were having an elective procedure where abdominal fat could be obtained. Surgical adipose tissue biopsies were immediately frozen in liquid nitrogen and stored at -80ºC until gene expression analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from adipose tissue samples using TRIzol reagent (Invitrogen, Carlsbad, CA). The integrity and concentration of RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Inc. Headquarter, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
1 μg of total RNA was amplified and labelled using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol without rRNA reduction.
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip Human Gene 1.0 ST arrays were hybridized with 11 μg of labeled sense DNA, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007).
|
| Scan protocol |
Array images were acquired using an Affymetrix GeneChip 3000 7G scanner
|
| Description |
pre-pubertal subcutaneous fat sample from an obese, male subject, replicate 4
|
| Data processing |
Raw CEL files were normalised using RMA, via the Affymetrix Power Tools, v 1.8.5
|
| |
|
| Submission date |
Jun 03, 2011 |
| Last update date |
Jun 04, 2011 |
| Contact name |
Mark Cowley |
| E-mail(s) |
m.cowley@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Genome Informatics & Clinical Genomics
|
| Lab |
Dinger lab
|
| Street address |
384 Victoria St.
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE29718 |
An early inflammatory gene profile in visceral adipose tissue in children |
|
