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Sample GSM1498293 Query DataSets for GSM1498293
Status Public on Mar 01, 2015
Title Animal # 43
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 12.6816
10338002 5.63447
10338003 10.6759
10338004 9.57878
10338005 2.02568
10338006 2.262
10338007 2.62582
10338008 3.35076
10338009 6.3502
10338010 2.13093
10338011 5.30048
10338012 2.19664
10338013 1.89778
10338014 2.00227
10338015 1.96024
10338016 6.10661
10338017 13.8054
10338018 5.85481
10338019 4.71894
10338020 6.69977

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM1498293_05-Animal43.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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