|
| Status |
Public on Feb 17, 2017 |
| Title |
D_PRE |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
subcutaneous adipose tissue, male, baseline
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: obese
gender: male
tissue: subcutaneous adipose tissue
treatment: hypo-caloric diet and moderate exercise
timepoint: pre-treatment
individual identifier: D
|
| Treatment protocol |
Subcutaneous adipose tissue biopsies were sampled at baseline and after the 15-week intervention. In short, a small incision was made in the skin after anesthetising with lidocaine (10 mg/mL). 10-15 g tissue was extracted by use of a needle with partial vacuum after injection of 15 mL isotonic NaCl into the subcutaneous adipose tissue. Biopsies were washed in isotonic NaCl and snap-frozen in liquid nitrogen and stored at -80°C immediately.
|
| Growth protocol |
13 severely obese individuals (seven women and six men) underwent a 15-week weight loss intervention including moderate daily exercise and a hypo-caloric diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from approximately 350 mg of subcutaneous adipose tissue using Trizol (Invitrogen, Carlsbad, CA, USA).
|
| Label |
Hy3
|
| Label protocol |
500 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| Channel 2 |
| Source name |
reference pool of subcutaneous adipose tissue
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Common references pool (equal pool of all test samples)
|
| Treatment protocol |
Subcutaneous adipose tissue biopsies were sampled at baseline and after the 15-week intervention. In short, a small incision was made in the skin after anesthetising with lidocaine (10 mg/mL). 10-15 g tissue was extracted by use of a needle with partial vacuum after injection of 15 mL isotonic NaCl into the subcutaneous adipose tissue. Biopsies were washed in isotonic NaCl and snap-frozen in liquid nitrogen and stored at -80°C immediately.
|
| Growth protocol |
13 severely obese individuals (seven women and six men) underwent a 15-week weight loss intervention including moderate daily exercise and a hypo-caloric diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from approximately 350 mg of subcutaneous adipose tissue using Trizol (Invitrogen, Carlsbad, CA, USA).
|
| Label |
Hy5
|
| Label protocol |
500 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| |
| Hybridization protocol |
The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 6th GEN (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 16.0.
|
| Scan protocol |
The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).
|
| Description |
D1
Hy3: 1_Exiqon_14326095_S01.txt
Hy5: 0_Exiqon_14326095_S01.txt
|
| Data processing |
The quantified signals were background corrected and normalised using LOESS in marray and linear models for microarray analysis (LIMMA).
Please note that only capture probes targeting human miRNAs as well as all control probes on the array platform were included during the normalization step. Following normalization, all control probes were removed and probe set level expression data were summarized for each human miRNA by the average value of the corresponding probe sets.
|
| |
|
| Submission date |
Sep 19, 2016 |
| Last update date |
Feb 19, 2017 |
| Contact name |
Malene Maag Kristensen |
| E-mail(s) |
malenemk@hotmail.com
|
| Organization name |
University of Copenhagen
|
| Street address |
Blegdamsvej 3
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL11434 |
| Series (1) |
| GSE87103 |
miRNAs in human subcutaneous adipose tissue: Effects of weight loss induced by hypo-caloric diet and exercise |
|
