Gene expression and VDJ profiling at single cell level of CD4 T cells isolated from the female reproductive tract (FRT) of Chlamydia muridarum infected WT (B6) and Bhlhe40-/- mice
CD4 T cells are recruited to the FRT following Chlamydia intravaginal infection.  We use single-cell RNA sequencing and VDJ profiling to compare CD4 T cells sorted from WT (B6) and Bhlhe40-/- mice at 14 days post Chlamydia muridarum intravaginal infection. Overall design: Activated CD4 T cells in the FRT of Chlamydia-infected WT (B6) and Bhlhe40-/- mice were sorted by fluorescence-activated cell sorting (FACS) according to CD4+, CD44hi and CD90.2+ expression, and the absence of CD11b, B220 and F4/80 expression.  Sorted cells were analyzed using scRNAseq.