Fast single-cell joint analysis of histone modifications and transcriptome by Droplet Paired-Tag

Analysis of histone modifications at single-cell resolution can provide insights into the cellular heterogeneity in activity states of regulatory elements. However, current methods are hindered by lengthy procedures and insufficient sensitivity. Here we present Droplet Paired-Tag, a microfluidic cell barcoding-based method for fast and robust joint analysis of histone modifications and gene expression from single cells. We applied Droplet Paired-Tag to mouse brain and demonstrated its utility in accurately identifying active or repressive regulatory elements, and resolving the dynamic interactions between candidate regulatory elements and putative target genes. Overall design: Combined analysis of RNA and histone modifcations in single-cells