|
| Status |
Public on Dec 29, 2011 |
| Title |
wt B6 CD4 T cells biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
CD4T cells from the spleen of wt B6 mice
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: wildtype
cell type: CD4T cells
strain: C57BL/6J
tissue: spleen
|
| Treatment protocol |
For CD69 activation after 24h cell culturing, anti-CD69 antibody (1:200 dilution) was added and after 48h cell culturing secoundary cross-linking antibody (1:200 dilution) was also added.
|
| Growth protocol |
107 CD4 enriched T cells in medium containing RPMI, 10%FCS and 1% Penicilin/Streptomycin were cultured with anti-CD3/anti-CD28 coated beads (cell:bead ratio 10:1) for 72h at 37°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared from peletted CD4 T cells using RNAeasy mini kit (Qiagen, Hilden, Germany)
|
| Label |
biotin
|
| Label protocol |
Whole Transcript (WT) Sense Target Labeling Assay
|
| |
|
| Hybridization protocol |
according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay
|
| Scan protocol |
according to Affymetrix protocols using a GeneChip 3000 Scanner
|
| Description |
gene expression data from CD4 T cells from the spleen of wt B6 mice
|
| Data processing |
Statistical analyses were carried out using R (v. 2.12.1) (R-Development-Core-Team, 2010). Arrays have been normalized using robust multiple-array average (RMA) (Gautier et al., 2004). Expression data were analyzed using Bioconductor oligo package for R (Benilton and Irizarry, 2010). Differentially expressed genes were determined by the shrinkage T-statistic (Opgen-Rhein and Strimmer, 2007). A one-way ANOVA test (for non-parametric) data and a t-test for two unequal variances was used. P < 0.05 was considered statistically significant.
|
| |
|
| Submission date |
Mar 07, 2011 |
| Last update date |
Dec 30, 2011 |
| Contact name |
Karlheinz Holzmann |
| E-mail(s) |
[email protected]
|
| Organization name |
Ulm University
|
| Department |
Medical Faculty
|
| Lab |
Genomics Core Facility
|
| Street address |
Helmholtzstreet 8/1
|
| City |
Ulm |
| ZIP/Postal code |
D-89081 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE27706 |
CD69-dependent gene expression in activated CD4 T cells from the spleen of Mus musculus |
|
