|
| Status |
Public on Sep 10, 2011 |
| Title |
Control, replicate 4 |
| Sample type |
RNA |
| |
|
| Source name |
Control, replicate 4
|
| Organism |
Mus musculus |
| Characteristics |
knockdown: Control
amplification date: 09/06/19
hybridization date: 09/06/29
colon length (mm): 7.8
colon weight (mg): 172
colon ratio (mg/mm): 2.21
myeloperoxidase activity (u/mg): 0.076
tissue: colon
treatment: 5% DSS
|
| Treatment protocol |
No additional treatment was used prior to RNA extraction
|
| Growth protocol |
anti-TNFa siRNA treatment in a mouse model of IBD: effects of various chemical modifications on clinical parameters and the inflammatory axis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using a RNEasy RNA extraction kit (Qiagen). Purity and integrity of the purified RNA was assessed on the Agilent Bioanalyzer 2100. Concentration was determined with a Nanodrop ND-1000 Spectrophotometer.
|
| Label |
biotin
|
| Label protocol |
25 ng total RNA per sample was used for Whole Transcriptome Amplification (Sigma) according to manufacturer´s recommendations. 10 microgram cDNA was fragmented, and biotinylated using Affymetrix' 10K v2 Assay Kit according to manufacturer's recommendations (http://www.affymetrix.com).
|
| |
|
| Hybridization protocol |
Hybridization of the samples to Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays were performed according to the manufacturer’s instructions (http://www.affymetrix.com).
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip@ Scanner 3000.
|
| Description |
The U of U/miligramsg stands for Unit of MPO activity. One unit of MPO activity was defined as the amount that degraded 1.0 umol of peroxide per min at 25 C.
|
| Data processing |
Gene expression data was pre-processed and normalized using Partek Genomics Suite. The data was quantile normalized, and the summarization was obtained via RMA.
|
| |
|
| Submission date |
Sep 06, 2011 |
| Last update date |
Sep 10, 2011 |
| Contact name |
Evarist Planet Letschert |
| E-mail(s) |
evarist.planet@irbbarcelona.org
|
| Organization name |
IRB Barcelona
|
| Department |
Biostatistics
|
| Street address |
C/ Baldiri Reixac 10
|
| City |
Barcelona |
| State/province |
Spain |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE31906 |
Genome wide gene expression profiles of distal colon from 5% DSS-treated mice after administration of various siRNA against TNFa. |
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