scATAC-seq over multiple time points of heart development in WT C57Bl6/J embryos and in Tbx1 mutant mice (Tbx1 KO)

We performed scATAC-seq over multiple time points of heart development in WT C57Bl6/J embryos and in Tbx1 mutant mice (Tbx1 KO). We dissected primarily the cardiac region but also the regions dorsal to the heart and the pharyngeal arches to capture the progenitor cells that migrate into the heart and the neural crest cells. For time points E10.5 and E11.5, we primarily dissected the regions behind the heart and included less of the overall cardiac region. We included pharyngeal arches for all time points and, at E11.5, we excluded the first arch. For Tbx1 null embryos, we also generated scRNA-seq data for WT and mutant embryos from the same pool of dissociated cells used for scATAC-seq. For all embryos, we micro-dissected the tissue and dissociated using TryplE and then proceeded with a nuclei isolation method according to manufacturer's instructions (10X Genomics, https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-isolation-of-nuclei-for-single-cell-rna-sequencing-and-tissues-for-single-cell-rna-sequencing). For all samples, multiple replicates for WT and KO were used and we include all replicates below.