Single-cell ftATACseq data of mouse thymocytes

This dataset is related to our recent study "APEC: an accesson-based method for single-cell chromatin accessibility analysis". We adopted a fluorescent tagmentation-based single-cell ATAC-seq technique (ftATAC-seq) to investigated the per cell regulome dynamics of mouse thymocytes. Associated with ftATAC-seq, APEC revealed a detailed epigenomic heterogeneity of thymocytes, characterized the developmental trajectory and predicted the regulators that control the stages of maturation process. To evaluate the performance of this approach in the context of the immune system, we adopted ftATAC-seq technology to investigate the regulome dynamics of the thymic development process. Coordinated with essential cell surface markers, we provided a in-depth classification of thymocytes than the conventional DN, DP, CD4SP and CD8SP stages based on single-cell chromatin status. By reconstructing the developmental pseudotime trajectory, we discovered a transitional stage before thymocytes bifurcate into CD4SP and CD8SP cells and inferred that one of the stages leads to cell apoptosis. Considering that more than 95% of DP cells undergo apoptosis as a programmed cell death process, our data suggested that before DP cells enter the final apoptotic state, there would already be some intracellular changes towards apoptosis at the chromatin level.