|
| Status |
Public on Jul 25, 2013 |
| Title |
Wild-type DN thymocytes rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
CD4-CD8 double negative thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 2 months
tissue: Thymus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNeasy Mini Kit (Qiagen).Approximately 300 ng of total RNA was labelled and hybridised to Illumina MouseWG-6 v2.0 Expression BeadChips (Illumina) according to Illumina standard protocols.
|
| Label |
Cy3
|
| Label protocol |
Standard Illumina labelling protocol
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
replicate 2
|
| Data processing |
Raw intensity values were background corrected and normalized by the neqc method. Probes were filtered as ‘not expressed’ if they failed to achieve a BeadStudio detection P value of 0.05 on at least three arrays. Manufacturer probe annotation was used. Linear models were fitted to genes using Bioconductor R package limma. Differences in expression were assessed with empirical Bayes moderated t-statistics. Genes were considered to have different expression if they achieved a false-discovery rate of less than 0.05 and also a fold change of no less than 1.5.
|
| |
|
| Submission date |
Jul 24, 2013 |
| Last update date |
Jul 25, 2013 |
| Contact name |
Wei Shi |
| E-mail(s) |
Wei.Shi@onjcri.org.au
|
| Organization name |
Olivia Newton-John Cancer Research Institute
|
| Street address |
145 Studley Road
|
| City |
Heidelberg |
| State/province |
Victoria |
| ZIP/Postal code |
3084 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6887 |
| Series (1) |
| GSE49164 |
Requirement for Lyl1 in a model of Lmo2-driven early T-cell precursor ALL |
|
