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Sample GSM1498292 Query DataSets for GSM1498292
Status Public on Mar 01, 2015
Title Animal # 33
Sample type RNA
 
Source name Tarsal joint with clinical score 3 arthritis in 1-2 weeks
Organism Mus musculus
Characteristics strain: DBA/1JBom
tissue: Whole tarsal joint
Treatment protocol Arthritis was induced in male DBA/1JBom mice by intradermal injection of 100 µl chicken collagen type II (CII) (2mg/ml) (Sigma) in Complete Freunds Adjuvans (CFA) (0,5mg/ml) (Sigma) on day 1 and boosted on day 21 with CII in Incomplete Freunds Adjuvans (IFA)(Sigma). The control group was not induced.
Extracted molecule total RNA
Extraction protocol mirVanaTM miRNA isolation kit (Ambion, Denmark) according to the manufacturers´ instructions
Label Biotin
Label protocol Labelled using the Pico amplification kit (Nugen, San Carlos, USA), according to the manufacturers´ instructions
 
Hybridization protocol The labelled samples were hybridized to the Mouse Gene 1.0 ST GeneChip array (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained with phycoerytrin-conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450
Scan protocol The arrays were scanned in the Affymetrix GeneArray® 3000 scanner
Data processing Arrays were normalized using standard RMA background correction and quantile normalization using the 'affy' package from bioconductor in R version 2.15. Significance of singular genes was assessed using an ANOVA approach across the different groups, and adjusted for multiple testing by estimating false discovery rates (FDR).
 
Submission date Sep 05, 2014
Last update date Mar 01, 2015
Contact name Thomas Litman
E-mail(s) tlitman@hotmail.com
Phone 4541851753
Organization name University of Copenhagen
Department ISIM
Street address Blegdamsvej 3C
City Copenhagen N
State/province Outside the US or Canada
ZIP/Postal code 2200
Country Denmark
 
Platform ID GPL6246
Series (1)
GSE61140 Expression data from mouse arthritis tarsal joints

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
10338001 12.9136
10338002 5.58288
10338003 11.0199
10338004 10.014
10338005 2.09677
10338006 2.2869
10338007 2.58546
10338008 3.32433
10338009 6.26979
10338010 2.102
10338011 5.2781
10338012 2.21552
10338013 1.94324
10338014 1.97697
10338015 1.96364
10338016 6.15831
10338017 13.8382
10338018 5.86642
10338019 4.6983
10338020 6.6115

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM1498292_04-Animall33.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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