|
| Status |
Public on Mar 04, 2019 |
| Title |
Sample3_Wild-type DN thymocytes rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
Wild-type DN thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57 BL/6
genotype/variation: wild type
age: 2-3 months
tissue: Thymus
cell type: sorted CD4-CD8 double-negative (DN) thymocytes
|
| 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 3
Sample3
|
| 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 one array. 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 greater than 2.
|
| |
|
| Submission date |
Oct 22, 2018 |
| Last update date |
Mar 04, 2019 |
| Contact name |
Wei Shi |
| E-mail(s) |
Wei.Shi2@monash.edu
|
| Organization name |
Monash University
|
| Street address |
Wellington Rd
|
| City |
Clayton |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6887 |
| Series (1) |
| GSE121641 |
The oncoprotein NUP98-HOXD13 (NHD13) induces thymocyte self-renewal via Lmo2/Lyl1 |
|
