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.
Microfluidic Chip Design
CAD design for both bead generation and droplet encapsulation microfluidic chips
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
HyDrop-ATAC Mapping With VSN
Pre-processing and mapping of HyDrop-ATAC 8.5k mouse mortex nuclei dataset using our VSN pipeline.
HyDrop-ATAC CisTopic Tutorial
Includes quality control, cell filtering, clustering, dimensionality reduction, batch-effect correction, gene activity scores, differentially accessible regions, …
HyDrop-RNA Mapping With STARSolo
Pre-processing and mapping of HyDrop-RNA 9.5k mouse mortex nuclei dataset using Alex Dobin’s STARsolo.