|
| Status |
Public on Mar 01, 2015 |
| Title |
Animal # 57 |
| Sample type |
RNA |
| |
|
| Source name |
Tarsal joint with clinical score 3 arthritis in 0-3 days
|
| 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
|
| Description |
excluded in analysis due to QC fail
|
| 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) |
[email protected]
|
| 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 |
|
