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. Overall design: 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.