Global gene expression changes in E9.5 cardiopharyngeal mesoderm (CPM) of Chd7 mutants versus controls
To investigate the role of Chd7 in the CPM we performed RNA-seq on two microdissections from Mesp1-Cre; Chd7 fl/fl (referred to as cKO) and control (Mesp1-Cre) embryos. The first involved the distal pharyngeal apparatus, i.e. arches two through six including the dorsal pericardial wall (DPW) which encompasses the SHF before these cells migrate to the poles of heart. For simplicity we refer to this dissection as “SHF” (we use inverted commas in this denotation to recognise the presence of other cell types). The second microdissection included the cells that have entered the heart (i.e. SHF-derived outflow tract (OFT), right ventricle (RV) and parts of the atrium, and FHF-derived left ventricle and atria). The OFT and heart tissue was collected from the same embryos (labelled “HEART”). Overall design: Comparative gene expression profiling analysis of RNA-seq data for SHF and HEART tissue, from cKO (Mesp1-Cre; Chd7 fl/fl) and control (Mesp1-Cre) embryos. Tissue from each embryo was processed individually and sequenced as a single sample. Each “SHF” sample originated from a single embryo, and similarly each “HEART” sample originated from a single heart and OFT.