RNA-seq of mouse Embryonic stem cells at different stages of embryoid body differentiation

Haematopoietic and endothelial cells derive from a subset of Flk-1 expressing cells. In vitro differentiation of mouse embryonic stem cells (mESCs) to embryoid bodies (EBs) recapitulate several aspects of early embryonic development, including the formation of a subset of Flk-1 expressing cells. By day 4 of EB differentiation, mesodermal lineages with distinct lineage potentials can be identified based on the expression of the two surface markers Flk-1 and Pdgfra. Cells expressing Flk-1 alone (Flk-1?/Pdgfra?) are enriched for haematoendothelial precursors, whereas double-positive cells (Flk-1?/Pdgfra?) are enriched for primitive/cardiac mesodermal lineages. Here we performed RNA sequencing at multiple stages of EB differentiation to identify genes potentially important for mesoderm specification towards the haematoendothelial lineages. Mouse ESCs were differentiated to embryoid bodies for 4 days, dissociated, stained for the Flk-1 and Pdgfra markers and Flk-1?/Pdgfra? and Flk-1?/Pdgfra? populations were sorted by FACS. RNA sequencing was performed at multiple stages of EB differentiation: day 0 (D0), day 2 (D2), day 4 (D4) and the two sorted populations (D4 Flk-1?/Pdgfra? and D4 Flk-1?/Pdgfra?).