ATAC-seq analysis of chromatin accessibility in Mbd3-null and control lymphoid progenitor cells

To determine the role of Mbd3/NuRD in lymphopoiesis, chromatin accessbility was analysed in purified populations of Mbd3-deleted and control lymphoid progenitor cells using the assay for transposase-accessible chromatin using sequencing (ATAC-seq). Mbd3-deficient and control lymphoid progenitors were isolated from mouse bone marrow and thymus by flow cytometry, including all-lymphoid progenitors (ALPs) and B cell-biased lymphoid progenitors (BLPs), pro-B cells and DN3b thymocytes. ATAC-seq was performed as previously described (Buenrostro et al (2013) Nat. Methods 10:1213) on two or three biologically independent samples of 500 cells. Chromatin accessibility scores were determined based on the density of reads across the genome.