|
| Status |
Public on Dec 31, 2014 |
| Title |
thymocyte_Foxp3pos_WT_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
thymus T-cells
|
| Organism |
Mus musculus |
| Characteristics |
sort_fraction: CD4+Foxp3+
genotype: Wild type
cell_type: T-cell
organ: thymus
|
| Treatment protocol |
thymocytes sorted for either CD4+Foxp3+ and CD4SPFoxp3-
|
| Growth protocol |
WT or floxed mice were orally administered tamoxifen dissolved in corn oil 4 times every other day (3mg/mice) over a period of 10 days to induce deletion of E-protein in vivo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified by Qiagen RNAeasy kit
|
| Label |
biotin
|
| Label protocol |
Illumina TotalPrep RNA Amplification Kit (Ambion)
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol with Illumina HiScan-SQ
|
| Description |
WT Foxp3KI mice
_9253995055_B
|
| Data processing |
Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset. After filtering probes, quantile normalization was applied across all arrays. ANOVA was performed on the normalized log2 expression estimates to test for mRNA expression differences by strain (wild type [WT] or knockout [KO] of E-proteins) and sort fraction (FoxP3+ or FoxP3-). A p-value of 0.05 was used for the statistical significance cutoff, after adjusting for the familywize error rate (FWER) using Benjamini–Hochberg method to account for multiple testing. Statistical analysis was performed using JMP/Genomics software version 6.0.
|
| |
|
| Submission date |
Oct 24, 2013 |
| Last update date |
Dec 31, 2014 |
| Contact name |
Timothy G Myers |
| E-mail(s) |
tgm@nih.gov
|
| Organization name |
National Institute of Allergy and Infectious Diseases
|
| Department |
Research Technologies Branch
|
| Lab |
Genomic Technologies Section
|
| Street address |
50 South Drive, Room 5509
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-8005 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE51654 |
Dynamic Changes in E-protein Activity are Essential for Treg cell Development |
|
