|
| Status |
Public on Sep 08, 2008 |
| Title |
Colon_NonTreated_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Colon Non-treated
|
| Organism |
Mus musculus |
| Characteristics |
Strain: SJL/J
Gender: male
Age: 6 weeks
Tissue: Colon
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
RNA labeling protocol available via www.vumc.nl/microarrays. Also described in Bergman et al, Cancer Res 2005; 65: (20). October 15, 2005
|
| |
|
| Channel 2 |
| Source name |
Common reference pool from pooled colon derived total RNA of treated and non-treated mice
|
| Organism |
Mus musculus |
| Characteristics |
Strain: SJL/J
Age: 6 weeks
Tissue: pooled colon
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
RNA labeling protocol available via www.vumc.nl/microarrays. Also described in Bergman et al, Cancer Res 2005; 65: (20). October 15, 2005
|
| |
|
| |
| Hybridization protocol |
Hybridization protocol available via www.vumc.nl/microarrays. Also described in Bergman et al, Cancer Res 2005; 65: (20). October 15, 2005
|
| Scan protocol |
Slides were scanned with the Agilent DNA Microarray Scanner (Agilent Technologies).
Spots were quantified by Imagene 5.5.4 software (Biodiscovery Ltd, Marina del Rey, CA, USA), using the default settings.
|
| Description |
Biological replicate 2 of 4 Non-treated
|
| Data processing |
The BioConductor package Limma (Smyth and Speed 2003) version 2.6.0 was used to perform data processing. Background correction according to 'Edwards' was applied with an offset of 30. Intensity-dependent normalization using local estimation (‘Loess’) was performed separately on each sector of the array. In addition, ‘scale’ (or ‘quantile’) normalization was applied, which makes the data more comparable across different arrays. Spots were included in the analysis when in at least 80% of the microarrays a reliable data point was obtained for that element (defined by a minimal signal intensity > 50 for both Cy3 and Cy5). Data are expressed as normalized log2 ratios of fluorescence intensities of the experimental over the reference sample. The use of a common reference sample allows comparison of the relative expression levels across all samples. Therefore, the expression levels were median centered, i.e. each spotted element was expressed relative to the median expression level of that element across all samples. Genes represented more than once on the microarrays were averaged from sequences with the same Unigene cluster ID.
|
| |
|
| Submission date |
Jul 17, 2008 |
| Last update date |
Sep 08, 2008 |
| Contact name |
Antonie Zwiers |
| E-mail(s) |
[email protected]
|
| Organization name |
Vrije Universiteit Medical Center
|
| Department |
MCBI
|
| Street address |
Van der Boechorststraat 7
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 BT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL2858 |
| Series (1) |
| GSE12139 |
Colonic tissues from an acute TNBS-induced colitis model in SJL mice. |
|
