Abstract

Single-cell RNA-seq and single-cell ATAC-seq technologies are 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 pave the way for more specialized multi-ome assays, custom droplet microfluidics may provide solutions complementary to commercial setups. We developed HyDrop, a flexible and open-source 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 7,996 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.

Data availability

The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE175684 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175684) and on SCope (https://scope.aertslab.org/#/HyDrop/*/welcome).Source Data files have been provided for figures 2a, 3a, 3b, 3c and 3i, and can be regenerated data analysis tutorials for HyDrop.Data analysis tutorials for HyDrop are available on GitHub (https://github.com/aertslab/hydrop_data_analysis).

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Florian De Rop

    VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5241-924X
  2. Joy N Ismail

    VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  3. Carmen Bravo González-Blas

    VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  4. Gert J Hulselmans

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  5. Christopher Campbell Flerin

    VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  6. Jasper Janssens

    VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  7. Koen Theunis

    VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  8. Valerie M Christiaens

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  9. Jasper Wouters

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7129-2990
  10. Gabriele Marcassa

    VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  11. Joris de Wit

    VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  12. Suresh Poovathingal

    VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
    For correspondence
    suresh.poovathingal@kuleuven.be
    Competing interests
    The authors declare that no competing interests exist.
  13. Stein Aerts

    VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
    For correspondence
    stein.aerts@kuleuven.be
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8006-0315

Funding

H2020 European Research Council (724226_cis- CONTROL)

  • Stein Aerts

VIB Tech Watch

  • Suresh Poovathingal

KU Leuven (C14/18/092)

  • Stein Aerts

Fonds Wetenschappelijk Onderzoek (G0B5619N)

  • Stein Aerts

Michael J. Fox Foundation for Parkinson's Research (ASAP-000430)

  • Christopher Campbell Flerin

Aligning Science Across Parkinson's (ASAP-000430)

  • Christopher Campbell Flerin

Foundation Against Cancer (2016-070)

  • Stein Aerts

Stichting tegen Kanker

  • Jasper Wouters

Belgian Cancer Society

  • Jasper Wouters

Fonds Wetenschappelijk Onderzoek

  • Florian De Rop
  • Carmen Bravo González-Blas
  • Jasper Janssens

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Naama Barkai, Weizmann Institute of Science, Israel

Ethics

Animal experimentation: All animal experiments were conducted according to the KU Leuven ethical guidelines and approved by the KU Leuven Ethical Committee for Animal Experimentation (approved protocol numbers ECD P037/2016, P014/2017, and P062/2017). All use of cell lines was approved by the KU Leuven Ethical Committee for Research under project number S63316.

Version history

  1. Preprint posted: June 6, 2021 (view preprint)
  2. Received: September 16, 2021
  3. Accepted: February 21, 2022
  4. Accepted Manuscript published: February 23, 2022 (version 1)
  5. Version of Record published: April 8, 2022 (version 2)
  6. Version of Record updated: April 13, 2022 (version 3)
  7. Version of Record updated: June 8, 2022 (version 4)
  8. Version of Record updated: October 2, 2023 (version 5)

Copyright

© 2022, De Rop et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Florian De Rop
  2. Joy N Ismail
  3. Carmen Bravo González-Blas
  4. Gert J Hulselmans
  5. Christopher Campbell Flerin
  6. Jasper Janssens
  7. Koen Theunis
  8. Valerie M Christiaens
  9. Jasper Wouters
  10. Gabriele Marcassa
  11. Joris de Wit
  12. Suresh Poovathingal
  13. Stein Aerts
(2022)
HyDrop enables droplet based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads
eLife 11:e73971.
https://doi.org/10.7554/eLife.73971

Share this article

https://doi.org/10.7554/eLife.73971

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