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Summary: 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.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Summary: Mouse embryonic stem cells (mESCs) can be directed to acquire cell-lineage-specific genetic programs and phenotypes by stepwise exposure to defined factors, allowing the development of in vitro models for studying disease and tissue generation. In this protocol, we describe the use of cultured mESCs to generate presomitic-like mesoderm cells undergoing further specification towards myogenic progenitors (MPs). Further, we describe here a procedure to obtain, dissect, and fluorescence-activated cell sorting (FACS)-isolate somitic cells from genetically labeled Pax7+/Cre; Rosa26YFP/+ embryos.For complete details on the use and execution of this protocol, please refer to Khateb et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Summary: It remains challenging to generate reproducible, high-quality cDNA libraries from RNA derived from rare cell populations. Here, we describe a protocol for high-throughput RNA-seq library preparation, including isolation of 200 skeletal muscle stem cells from mouse tibialis anterior muscle by fluorescence-activated cell sorting and cDNA preparation. We also describe RNA extraction and cDNA preparation from differentiating mouse embryonic stem cells.For complete details on the use and execution of this protocol, please refer to Juan et al. (2016) and Garcia-Prat et al. (2016).