Integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells.

Here, we present workflows for integrating independent transcriptomic and chromatin accessibility datasets and analyzing multiomics. First, we describe steps for integrating independent transcriptomic and chromatin accessibility measurements. Next, we detail multimodal analysis of transcriptomes and chromatin accessibility performed in the same sample. We demonstrate their use by analyzing datasets obtained from mouse embryonic stem cells induced to differentiate toward mesoderm-like, myogenic, or neurogenic phenotypes. For complete details on the use and execution of this protocol, please refer to Khateb et al..