|
| Status |
Public on Feb 04, 2012 |
| Title |
C-Ig_day3_mouse1 (technical replicate) |
| Sample type |
RNA |
| |
|
| Source name |
naive CD4+ T cells, control, day 3
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/NCrl
tissue: inguinal, axillary and brachial lymph nodes and spleen
cell type: naive CD4+ T cells
stimulus: control Ig
timepoint: day 3
mouse: 1
|
| Treatment protocol |
Mouse CD62L+CD44-CD25-DX5-CD4+ T cells were stimulated with plate-bound anti-CD3e (10ug/ml), soluble anti-CD28 (1ug/ml) in the presence of plate-bound Delta4-Ig or control Ig (each at 5ug/ml).
|
| Growth protocol |
Cells were grown in IMDM with 10% FCS, 2mM GlutaMAX (Invitrogen), 100 U/ml penicillin (Invitrogen), 100 μg/ml streptomycin (Invitrogen) and 50μM β-Mercaptoethanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol followed by purification with RNeasy columns.
|
| Label |
biotin
|
| Label protocol |
Total RNA samples were amplified and biotinylated using the Ambion Illumina TotalPrep RNA Amplification Kit.
|
| |
|
| Hybridization protocol |
Whole Genome Expression with IntelliHyb Seal.
|
| Scan protocol |
Standard Illumina scanning protocol using the Illumina HiScan.
|
| Description |
5773678088_D
|
| Data processing |
Array data were extracted using Illumina's GenomeStudio software. Normalization and statistical analyses were carried out using Bioconductor packages in the statistical software package R. We performed normexp-by-control background correction, quantile normalization and log2 transformation on the Illumina sample and control probe profiles using the limma package. Probes that were not expressed (detection p-value < 0.05) on any of the arrays were filtered out. The arrayQualityMetrics package was used to ensure that the microarray data was of good quality. The normalized intensities of technical replicate arrays were averaged. Differential expression between the DLL4-Fc activated and control-Ig samples was assessed via a paired moderated t-test using the limma package.
|
| |
|
| Submission date |
Feb 03, 2012 |
| Last update date |
Feb 04, 2012 |
| Contact name |
Derk Amsen |
| E-mail(s) |
D.Amsen@amc.nl
|
| Phone |
0031205664977
|
| Organization name |
AMC
|
| Street address |
Meibergdreef 9
|
| City |
Amsterdam |
| ZIP/Postal code |
1105AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE35547 |
Notch controls the magnitude of CD4+ T cell responses by promoting cellular longevity |
|
