|
| Status |
Public on Aug 08, 2012 |
| Title |
wt_rep4 |
| Sample type |
RNA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
age: 8-12 weeks
strain: C57/bl6-129sv
genotype/variation: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
8-12 weeks old mouse lymphocytes from 3 KO and 3 littermate control C57/bl6-129sv mice were mechanically extracted from thymus. Total RNA was extracted by MirVana kit (Ambion) and treated with DNAse (Turbo DNA free kit, Ambion), following manufacturer instructions. Quality control for RNA integrity was performed by capillary electrophoresis on Agilent 2100 Bioanalyzer,
|
| Label |
biotin
|
| Label protocol |
100 ng of RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit (Ambion)
|
| |
|
| Hybridization protocol |
Hybridization on Mouse WG 6 v2 expression arrays (Illumina) was carried out according to the manufacturer’s instructions
|
| Scan protocol |
Scanning was carried out according to the manufacturer’s instructions
|
| Data processing |
Data were normalized and analyzed using Illumina Beadstudio 3.1.3 (background correction and quantile normalization)
Expression profiles of each sample were imported into GeneSpringGX 7.3.1 (Agilent Technologies, USA).
In addition to expression values, Illumina BeadStudio software computes a detection p-value. Based on this, each probe was assigned a detection flag (P (present): p < 0.045; M (Marginal): p between 0.050 and 0.045, A (Absent): p>0.05). Expression values below a defined threshold (i.e. 20) are set to the threshold in order to remove negative values after background correction. To identify dysregulated genes in KO mice, t-test and/or ANOVA and additional steps of filtering were carried out.
|
| |
|
| Submission date |
Dec 14, 2011 |
| Last update date |
Aug 08, 2012 |
| Contact name |
Francesca R. Santoni de Sio |
| E-mail(s) |
[email protected]
|
| Organization name |
San Raffaele Scientific Institute
|
| Department |
SR-TIGET
|
| Lab |
Mechanisms of Peripheral Tolerance
|
| Street address |
via Olgettina 58
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6887 |
| Series (2) |
| GSE34447 |
Gene expression analysis of wild type and KAP1 KO mouse T cell progenitors |
| GSE38580 |
KAP1 regulates gene networks controlling T cell development and activation |
|
