FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression [ATAC-seq]

We used single cell Assay for Transposase-Accessible Chromatin with high-throughput sequencing (scATAC-seq) to generate chromatin accessibility profiles of mouse splenic regulatory T cells from B6 mice. Overall design: Splenic regulatory T cells (CD4+, TCRß+, FoxP3-IRES-GFP+) and T conventional cells (CD4+, TCRß+, FoxP3-IRES-GFP-) were sorted from 6-8 week old B6 FoxP3-IRES-GFP mice into DMEM + 2% FCS, then resuspended in PBS + 0.04% BSA. Nuclei isolation, transposition, GEM generation, and library construction targeting capture of ~12000 cells (75% Tregs, 25% Tconv) were carried out as detailed in the Chromium Next GEM Single Cell ATAC manual (10x Genomics). Libraries were pooled and sequenced on an Illumina NovaSeq to a final median depth of approximately 30,000 reads per cell (~80% saturation).