HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

We developed HyDrop, a new droplet microfluidic single-cell sequencing protocol for single-cell ATAC-seq and single-cell RNA-seq. We applied HyDrop-ATAC to flash-frozen mouse cortex and generated 7996 single-cell chromatin accessibility profiles. We applied HyDrop-RNA to flash-frozen mouse cortex and generated 9508 single-cell transcriptomes. We also applied HyDrop-RNA to a small population of FAC-sorted neurons from the Drosophila brain to demonstrate the protocol's applicability to low-input samples. The data available in this repository can be used to replicate all the figures in our manuscript using our data analysis tutorial available here: https://github.com/aertslab/hydrop_data_analysis Overall design: HyDrop-ATAC on mixed species cell lines and mouse cortex nuclei. HyDrop-RNA on mixed-species cell lines, mouse cortex nuclei and FAC-sorted drosophila neurons.