|
| Status |
Public on Feb 01, 2011 |
| Title |
Subject24_before |
| Sample type |
RNA |
| |
|
| Source name |
Human colon biopsies before intervention
|
| Organism |
Homo sapiens |
| Characteristics |
subject number: Subject24
disease status: IBD
gender: female
age: 40
intervention status: before
|
| Treatment protocol |
Subjects with a before AND after measurement participated in a 7-day red meat intervention study (300 grams of red meat per day). Subjects with only a before measurement did not participate in any intervention
|
| Extracted molecule |
total RNA |
| Extraction protocol |
During a colonoscopic examination six biopsies were taken from mucosal tissue in visually non-inflamed regions of the colon (in most cases from the sigmoid and descending colon) which were immediately frozen in liquid nitrogen and stored at -80 °C until use. Three biopsies were separately dissolved in QIAzol® (Qiagen, Venlo, The Netherlands) using a tissue disruptor and subsequently pooled. Total RNA was subsequently extracted according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Dye-labeled cRNA (Cy3) was synthesized following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies, Amstelveen, The Netherlands).
|
| |
|
| Hybridization protocol |
Hybridization according to Agilent instructions on 4x44K human whole genome microarrays.
|
| Scan protocol |
Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 was excited at a wavelengths of 532 nm. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 522 (Cy3), based on automatic establishment of ideal scan settings. Images were subsequently saved (resolution 5 micron, 16 bit tiff image).
|
| Description |
No intervention
|
| Data processing |
Bad and empty spots were flagged using the GenePix Pro software (version 6.0, Molecular Devices, Sunnyvale, CA). Quality control was performed in the statistical software environment R (version 2.10.1, The R Foundation for Statistical Computing, Vienna, Austria). Quantile normalization and subsequent data processing including background subtraction and Log2 transformation of spot intensities was performed in ArrayTrack (version 3.4, NCTR, Jefferson, AR).
|
| |
|
| Submission date |
Nov 09, 2010 |
| Last update date |
Feb 01, 2011 |
| Contact name |
Dennie Hebels |
| E-mail(s) |
d.hebels@maastrichtuniversity.nl
|
| Phone |
0031-43-3881088
|
| Fax |
0031-43-3884146
|
| URL |
http://www.grat.nl
|
| Organization name |
Maastricht University
|
| Department |
Health Risk Analysis and Toxicology
|
| Street address |
Universiteitssingel 50
|
| City |
Maastricht |
| ZIP/Postal code |
6200MD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE25220 |
Transcription levels in human colon biopsies in IBS and IBD patients before and after participating in a high red-meat dietary intervention |
|
