Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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

View ORCID ProfileFlorian V. De Rop, View ORCID ProfileJoy N. Ismail, View ORCID ProfileCarmen Bravo González-Blas, View ORCID ProfileGert J. Hulselmans, View ORCID ProfileChristopher C. Flerin, View ORCID ProfileJasper Janssens, View ORCID ProfileKoen Theunis, Valerie M. Christiaens, View ORCID ProfileJasper Wouters, View ORCID ProfileGabriele Marcassa, View ORCID ProfileJoris de Wit, View ORCID ProfileSuresh Poovathingal, View ORCID ProfileStein Aerts
doi: https://doi.org/10.1101/2021.06.04.447104
Florian V. De Rop
1VIB-KU Leuven Center for Brain & Disease Research
2Laboratory of Computational Biology, Department of Human Genetics, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Florian V. De Rop
Joy N. Ismail
1VIB-KU Leuven Center for Brain & Disease Research
2Laboratory of Computational Biology, Department of Human Genetics, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Joy N. Ismail
Carmen Bravo González-Blas
1VIB-KU Leuven Center for Brain & Disease Research
2Laboratory of Computational Biology, Department of Human Genetics, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Carmen Bravo González-Blas
Gert J. Hulselmans
1VIB-KU Leuven Center for Brain & Disease Research
2Laboratory of Computational Biology, Department of Human Genetics, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Gert J. Hulselmans
Christopher C. Flerin
1VIB-KU Leuven Center for Brain & Disease Research
2Laboratory of Computational Biology, Department of Human Genetics, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Christopher C. Flerin
Jasper Janssens
1VIB-KU Leuven Center for Brain & Disease Research
2Laboratory of Computational Biology, Department of Human Genetics, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jasper Janssens
Koen Theunis
1VIB-KU Leuven Center for Brain & Disease Research
2Laboratory of Computational Biology, Department of Human Genetics, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Koen Theunis
Valerie M. Christiaens
1VIB-KU Leuven Center for Brain & Disease Research
2Laboratory of Computational Biology, Department of Human Genetics, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jasper Wouters
1VIB-KU Leuven Center for Brain & Disease Research
2Laboratory of Computational Biology, Department of Human Genetics, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jasper Wouters
Gabriele Marcassa
1VIB-KU Leuven Center for Brain & Disease Research
3Laboratory of Synapse Biology, Department of Neurosciences, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Gabriele Marcassa
Joris de Wit
1VIB-KU Leuven Center for Brain & Disease Research
3Laboratory of Synapse Biology, Department of Neurosciences, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Joris de Wit
Suresh Poovathingal
1VIB-KU Leuven Center for Brain & Disease Research
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Suresh Poovathingal
  • For correspondence: suresh.poovathingal@kuleuven.be stein.aerts@kuleuven.be
Stein Aerts
1VIB-KU Leuven Center for Brain & Disease Research
2Laboratory of Computational Biology, Department of Human Genetics, KU Leuven
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Stein Aerts
  • For correspondence: suresh.poovathingal@kuleuven.be stein.aerts@kuleuven.be
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

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 Statement

The authors have declared no competing interest.

Footnotes

  • ↵# Shared last author

  • https://hydrop.aertslab.org

  • https://www.protocols.io/workspaces/aertslab

  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175684

  • https://scope.aertslab.org/#/HyDrop/

  • https://github.com/aertslab/hydrop_data_analysis

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted June 06, 2021.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads
Florian V. De Rop, Joy N. Ismail, Carmen Bravo González-Blas, Gert J. Hulselmans, Christopher C. Flerin, Jasper Janssens, Koen Theunis, Valerie M. Christiaens, Jasper Wouters, Gabriele Marcassa, Joris de Wit, Suresh Poovathingal, Stein Aerts
bioRxiv 2021.06.04.447104; doi: https://doi.org/10.1101/2021.06.04.447104
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads
Florian V. De Rop, Joy N. Ismail, Carmen Bravo González-Blas, Gert J. Hulselmans, Christopher C. Flerin, Jasper Janssens, Koen Theunis, Valerie M. Christiaens, Jasper Wouters, Gabriele Marcassa, Joris de Wit, Suresh Poovathingal, Stein Aerts
bioRxiv 2021.06.04.447104; doi: https://doi.org/10.1101/2021.06.04.447104

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3686)
  • Biochemistry (7766)
  • Bioengineering (5666)
  • Bioinformatics (21234)
  • Biophysics (10552)
  • Cancer Biology (8157)
  • Cell Biology (11902)
  • Clinical Trials (138)
  • Developmental Biology (6736)
  • Ecology (10387)
  • Epidemiology (2065)
  • Evolutionary Biology (13838)
  • Genetics (9693)
  • Genomics (13054)
  • Immunology (8120)
  • Microbiology (19932)
  • Molecular Biology (7824)
  • Neuroscience (42955)
  • Paleontology (318)
  • Pathology (1276)
  • Pharmacology and Toxicology (2256)
  • Physiology (3350)
  • Plant Biology (7207)
  • Scientific Communication and Education (1309)
  • Synthetic Biology (1998)
  • Systems Biology (5528)
  • Zoology (1126)