ATAC-seq of in vitro differentiated naïve, Th1, and Th9 cells

To investigate changes in chromatin accessibility over time, we differentiated Th9 cells in vitro from naïve T cells from human and murine sources, and followed them over an extended time course, during which they gained and then lost capacity for IL-9 production Overall design: We then performed Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) on cells from 2 different human donors and from 2 mice at 4 time points. In a separate experiments, we performed ATAC-seq on in vitro differentiated Th1 cells from human donors, which were sorted based on CXCR3 and CCR4 expression Peaks called relative to background, using MACS1.4