Identification of open chromatin regions in mouse cardiopharyngeal mesoderm

In the heart development, mesodermal progenitor cells in pharyngeal apparatus, termed cardiopharyngeal mesoderm, contribute to both atruim and right ventricle. Tbx1 gene, encoding a T-box transctiption factor and gene haploinsufficient in 22q11.2 deletion syndrome, is required for cardiac outflow tranct and branchiomeric muscle development. To understand how TBX1 affect open chromatin status in cardiopharyngeal mesoderm, we performed ATAC-seq in Tbx1-Cre lineage with/without Tbx1 expression. Overall design: Tbx1 gene expressed in pharyngeal apparatus from E8.5 to E10.5 including mesoderm, endoderm and ectoderm.We collected GFP positive cell from Tbx1-Cre/+;GFPflox/+ embryos (control) and Tbx1-Cre/flox;GFPflox/+ embryos (conditional knockout) at E9.5 for ATAC-seq. To extract ATAC-seq peaks in mesodermal cells, we also perfomed ATAC-seq in sorted GFP positive cell from Mesp1-Cre/+;GFPflox/+ embryos at E9.5 then open chromatin regions found in both Tbx1-Cre lineage and Mesp1-Cre lineage were used for analysis.