HyDrop
An open-source droplet microfluidics platform for single-cell RNA-seq and single-cell ATAC-seq inspired by inDrop and Drop-seq. Developed at Aerts lab in close collaboration with the Single cell and Microfluidics Expertise Unit at the VIB Center for Brain and Disease Research. Published at eLife in 2022!
Lab setup and requirements
We use Droplet Genomics' Onyx integrated microfluidic instrument to perform both hydrogel bead generation as well as the HyDrop-ATAC and HyDrop-RNA cell encapsulations. While the Onyx provides a ready-to-use package out of the box (setup takes only about 5 minutes), we have also worked with custom Cetoni and harvard pump setups. Both approaches can work well, although the latter solution will require more hands-on finetuning and experimentation. In terms of plasticware and reagent consumption, a HyDrop-ATAC or -RNA experiment can be performed for ~$0.03 - $0.05 per cell. Detailed protocols describing the chip/bead manufacturing process as well as a step-by-step tutorial for HyDrop-ATAC and HyDrop-RNA can be found below.
Hands-on Protocols
Datasets
Several datasets are available for download. We have performed HyDrop-ATAC on mouse/human species-mixed samples as well as on 8.5k mouse cerebral cortex nuclei. HyDrop-RNA data is available for species-mixed samples, 9500 mouse cerebral cortex nuclei and 973 FAC sorted fly neurons. These datasets are also used in the HyDrop data analysis tutorials.
GEO
