RNA-seq analysis of T cells with persistent Foxp3 transcriptional dynamics using Foxp3-Timer mice (Foxp3-Tocky)

We grouped Foxp3+ cells from Foxp3 Timer reporter mice into Blue1, Blue2, Red1, and Red2, and sorted these cells according to their Timer fluorescence expression, and analysed the transcriptional profiles of those cells, comparing them with those of effector and naive T cells using RNA-seq. Foxp3 Timer reporter mice were sensitised by a hapten, and 5 days later, the draining LNs of the skin were analysed. Foxp3Timer mice were sensitised with application of 3% Oxazolone to abdominal skin. 5 days later inguinal and axillary Lymph nodes were harvested and pooled within the 3 biological replicates. The following populations of T-cells were sorted from each mouse: 1. CD44loFoxp3Timer- (Naïve T-cells) 2. CD44hiFoxp3Timer- (Activated effector T-cells) 3. CD4+ Pers1 (BL1, persistent Foxp3 transcription) 4. CD4+ Pers2 (BL2, persistent Foxp3 transcription) 5. CD4+ PAt (RD1, quiescent Treg) 6. CD4+ Arrested (RD2, arrested Foxp3 transcription) RNA was extracted and RNA-seq data obtained, generating a triplicate dataset for the 6 T-cell populations.