Single-cell epigenomics and high-density genetic variation resolve the architecture of the Treg regulatory network [scATAC-seq]

To systematically examine the transcription factors and cis-regulatory elements that shape diverse Treg regulatory programs, we used single-cell Assay for Transposase-Accessible Chromatin with high-throughput sequencing (scATAC-seq) to generate chromatin accessibility profiles of mouse regulatory and conventional T cells from different organs and genetic backgrounds. Overall design: T regulatory (Treg) and conventional (Tconv) cells were sorted from either different organs (spleen, colon), genetic backgrounds (B6, B6/Cast F1), or different transcription factor knockouts (FoxP3, Gata3) for analysis by scATAC-seq