RT Journal Article
SR Electronic
T1 HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.06.04.447104
DO 10.1101/2021.06.04.447104
A1 Florian V. De Rop
A1 Joy N. Ismail
A1 Carmen Bravo González-Blas
A1 Gert J. Hulselmans
A1 Christopher C. Flerin
A1 Jasper Janssens
A1 Koen Theunis
A1 Valerie M. Christiaens
A1 Jasper Wouters
A1 Gabriele Marcassa
A1 Joris de Wit
A1 Suresh Poovathingal
A1 Stein Aerts
YR 2021
UL http://biorxiv.org/content/early/2021/06/06/2021.06.04.447104.abstract
AB Single-cell RNA-seq and single-cell ATAC-seq technologies are being used extensively to create cell type atlases for a wide range of organisms, tissues, and disease processes. To increase the scale of these atlases, lower the cost, and allow for more specialized multi-ome assays, custom droplet microfluidics may provide complementary solutions to commercial setups. We developed HyDrop, a flexible and generic droplet microfluidic platform encompassing three protocols. The first protocol involves creating dissolvable hydrogel beads with custom oligos that can be released in the droplets. In the second protocol, we demonstrate the use of these beads for HyDrop-ATAC, a low-cost non-commercial scATAC-seq protocol in droplets. After validating HyDrop-ATAC, we applied it to flash-frozen mouse cortex and generated 8,502 high-quality single-cell chromatin accessibility profiles in a single run. In the third protocol, we adapt both the reaction chemistry and the capture sequence of the barcoded hydrogel bead to capture mRNA, and demonstrate a significant improvement in throughput and sensitivity compared to previous open-source droplet-based scRNA-seq assays (Drop-seq and inDrop). Similarly, we applied HyDrop-RNA to flash-frozen mouse cortex and generated 9,508 single-cell transcriptomes closely matching reference single-cell gene expression data. Finally, we leveraged HyDrop-RNA’s high capture rate to analyse a small population of FAC-sorted neurons from the Drosophila brain, confirming the protocol’s applicability to low-input samples and small cells. HyDrop is currently capable of generating single-cell data in high throughput and at a reduced cost compared to commercial methods, and we envision that HyDrop can be further developed to be compatible with novel (multi-) omics protocols.Competing Interest StatementThe authors have declared no competing interest.