SHARE-seqV2 for single-cell epigenomic and transcriptomic mapping of human hematopoiesis at scale

A growing body of single-cell multi-omic tools enables a better understanding of gene regulation underlying development and disease. Tools mapping chromatin and gene expression (such as SHARE-seq) are limited in sensitivity and scalability. Here, we describe SHARE-seqV2 and its associated cloud-computing resource, enabling single-cell analysis at improved quality, robustness, and scale. We apply SHARE-seqV2 across various cell lines, primary tissues, and immune cells, demonstrating a generalizable platform for single-cell multi-omics. SHARE-seqV2 to profile chromatin accessibility and gene expression in the same cell from cell lines (HEK and 3T3), mouse colon, cultured HSC, and primey BMMC.