|
| Status |
Public on Sep 18, 2012 |
| Title |
Scurfy-CD4-LN-Biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
FACS sorted CD4+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: Scurfy (Sf; B6.Cg-Foxp3sf/J)
sex: male
age: 3-week old
tissue: peripheral lymph nodes
|
| Treatment protocol |
Three week old mice of various genotype were sacrificed and the peripheral lymph nodes were isolated. Axillary, brachial, inguinal, cervical and facial lymph nodes (LN) from sex- and age-matched B6, Sf, and Sf.Il2-/- mice were isolated, pooled, and single cell suspensions were prepared in PBS. CD4+ T cells were purified by depletion using biotinylated antibodies against B220, CD8, CD11b, CD11c and NK1.1 and magnetic beads (Miltenyi Biotec). The CD4-enriched cells were labeled with PE-anti-CD3 and Allophycocyanin (APC)-anti-CD4 antibodies and sorted at the UVA Flow Core facility by Fluorescence Assisted Cell Sorting (FACS) on a BD –Vantage cell sorter equipped with BD-Diva software. The purity of CD4+ T-cells was >99%.
|
| Growth protocol |
Three weeks old mice C57BL/6, Scurfy (Sf; B6.Cg-Foxp3sf/J) and Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) - termed as Sf.Il2-/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Rneasy miniprep kit (Qiagen) with on-column DNase digestion following manufacturer's protocol.
|
| Label |
Biotin
|
| Label protocol |
RNA was processed and labeled according to the standard target labeling protocols compatible with Affymetrix chips.
|
| |
|
| Hybridization protocol |
The samples were hybridized and stained per standard Affymetrix protocols at University of Virginia DNA sciences core facility. Mouse_430_2 arrays (Affymetrix, CA) were used for hybridization.
|
| Scan protocol |
The samples were scanned at Unversity of Virginia DNA sciences core using Affymetrix set-up.
|
| Description |
Gene expression data from Foxp3 mutant Scurfy (Sf) mice
|
| Data processing |
The data were The data were normalized using GC-RMA algorithm with software RMAExpress. Additionally analysis were performed using dChip, GCOS, R-statistical software equipped with LPE (Local Pooled Error) and SAM (Significance of Microarray) Bio-conductor packages.
|
| |
|
| Submission date |
Aug 03, 2010 |
| Last update date |
Sep 18, 2012 |
| Contact name |
Rahul Sharma |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Virginia
|
| Department |
Center for Immunity, Inflammation and Regenerative Medicine
|
| Street address |
Room 5768, Old Medical School Building, 21 Hospital Drive
|
| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE23398 |
IL-2 regulated genes in scurfy CD4+ T-cells |
|
