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Sample GSM790934 Query DataSets for GSM790934
Status Public on Sep 10, 2011
Title TNFa-OMe siRNA-B, replicate 6
Sample type RNA
 
Source name TNFa-OMe siRNA-B, replicate 6
Organism Mus musculus
Characteristics knockdown: TNFa-OMe siRNA-B
amplification date: 09/06/22
hybridization date: 09/06/30
colon length (mm): 5.7
colon weight (mg): 172
colon ratio (mg/mm): 3.02
myeloperoxidase activity (u/mg): 0.932
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.

Data table header descriptions
ID_REF
VALUE log2 RMA gene expression estimate.

Data table
ID_REF VALUE
10344614 9.85786
10344616 5.2263
10344618 5.27294
10344620 5.91349
10344622 9.25563
10344624 8.81822
10344633 10.4796
10344637 9.51832
10344653 6.40503
10344658 8.89849
10344674 5.91693
10344679 7.38001
10344705 9.63584
10344707 9.398
10344713 9.42594
10344715 6.4697
10344717 5.79513
10344719 8.07231
10344721 5.14058
10344723 8.2378

Total number of rows: 28853

Table truncated, full table size 475 Kbytes.




Supplementary file Size Download File type/resource
GSM790934_SOJune09--509-2009--30.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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