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Status |
Public on Sep 10, 2011 |
Title |
TNFa-OMe siRNA-B, replicate 3 |
Sample type |
RNA |
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Source name |
TNFa-OMe siRNA-B, replicate 3
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Organism |
Mus musculus |
Characteristics |
knockdown: TNFa-OMe siRNA-B amplification date: 09/06/19 hybridization date: 09/06/30 colon length (mm): 6 colon weight (mg): 172 colon ratio (mg/mm): 2.87 myeloperoxidase activity (u/mg): 0.384 tissue: colon treatment: 5% DSS
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Treatment protocol |
No additional treatment was used prior to RNA extraction
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Growth protocol |
anti-TNFa siRNA treatment in a mouse model of IBD: effects of various chemical modifications on clinical parameters and the inflammatory axis.
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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.
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Label |
biotin
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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).
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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).
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Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip@ Scanner 3000.
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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.
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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.
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Submission date |
Sep 06, 2011 |
Last update date |
Sep 10, 2011 |
Contact name |
Evarist Planet Letschert |
E-mail(s) |
evarist.planet@irbbarcelona.org
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Organization name |
IRB Barcelona
|
Department |
Biostatistics
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Street address |
C/ Baldiri Reixac 10
|
City |
Barcelona |
State/province |
Spain |
ZIP/Postal code |
08028 |
Country |
Spain |
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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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