|
| Status |
Public on Dec 08, 2011 |
| Title |
B6 thymic NKT 1 |
| Sample type |
RNA |
| |
|
| Source name |
Sorted NKT cells replicate 1
|
| Organism |
Mus musculus |
| Characteristics |
genetic background: C57BL/6
genotype: wt
source organ: thymus
cell type: NKT cells
|
| Treatment protocol |
Single cell suspensions from 10 pooled thymi were enriched for T cells by MACS using PanT cell isolation kit (Miltenyi). NKT cells (CD3e+CD1d tetramer+) were then purified by flow sorting (FACSAria, Becton-Dickinson) from the enriched T cells.
|
| Growth protocol |
Frest isolated NKT cells from indicated mouse strains
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using a Qiagen Qiashredder followed by the Qiagen RNeasy kit according to the manufacturer's instructions. RNA yield was quantified spectrophotometrically (Nanodrop ND-1000) and aliquots electrophoresed to determine sample purity and concentration (Agilent 2100 Bioanalyzer).
|
| Label |
Cy3
|
| Label protocol |
standard Agilent protocol
|
| |
|
| Hybridization protocol |
Hybridizations were performed using One-colour hybridization on SurePrint G3 Mouse GE 60k Microarray (Agilent)
|
| Scan protocol |
Slides were scanned using a GenePix 4000B Microarray scanner (Molecular Devices)
|
| Description |
Gene expression of sorted thymic wildtype NKT cells
|
| Data processing |
Images were processed with Agilent Feature Extraction software to generate raw probe intensity data, which was subsequently normalised by the quantile method. Differential expression analysis was carried out with an empirical Bayes approach on linear model using limma package.
|
| |
|
| Submission date |
Oct 03, 2011 |
| Last update date |
Dec 08, 2011 |
| Contact name |
Joyce Sebastian |
| E-mail(s) |
sebastian.joyce@vanderbilt.edu
|
| Phone |
615-322-1472
|
| Organization name |
Vanderbilt University School of Medicine
|
| Department |
Department of Microbiology and Immunology
|
| Street address |
A-4223 Medical Centre North
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL13912 |
| Series (1) |
| GSE32568 |
Gene expression comparison of wild-type and IL15ko thymic NKT cells |
|
