|
| Status |
Public on Aug 03, 2012 |
| Title |
PBMC_172_MED_final |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood mononuclear cells (PBMCs), after intervention (final)
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 40-65 yrs
health state: Abdominally overweight
cell type: peripheral blood mononuclear cells
diet: Mediterranean
|
| Treatment protocol |
Subjects consumed a completely controlled saturated fat (SFA)-rich diet, a SFA-by-MUFA-replaced diet (MUFA diet) or a MED diet for 8 weeks. Peripheral mononuclear cells PBMCs were collected before and after intervention.
|
| Growth protocol |
Abdominally overweight subjects, both males and females aged between 45-60 years, participated in this study. All subjects gave written informed consent to participate in the study and the study protocol was approved by the Medical Ethical Committee of Wageningen University, the Netherlands.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PBMCs were isolated from fasting whole blood samples by using the BD Vacutainer Cell Preparation Tubes. Total RNA was isolated of all PBMC samples by using the Qiagen RNeasy Micro kit (Qiagen, Venlo, Netherlands). The RNA yield was quantified with a Nanodrop ND 1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE), and RNA integrity was checked on an Agilent 2100 bioanalyzer with RNA 6000 Nano chips (Agilent Technologies, South Queensferry, United Kingdom). Samples were only accepted for microarray analyzes if the RNA integrity number (RIN) was > 8.
|
| Label |
biotin
|
| Label protocol |
The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol was conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
|
| Scan protocol |
Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
|
| Data processing |
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Affy'.
|
| |
|
| Submission date |
Jul 08, 2011 |
| Last update date |
Aug 03, 2012 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
[email protected]
|
| Organization name |
Wageningen University
|
| Department |
Div. Human Nutrition & Health
|
| Lab |
Nutrition, Metabolism & Genomics Group
|
| Street address |
HELIX, Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL7020 |
| Series (1) |
| GSE30509 |
Effects of a diet high in monounsaturated fat and a full Mediterranean diet on PBMC whole genome gene expression and plasma proteins |
|
