spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content Article Swipe
Joachim De Jonghe
,
Tomasz S. Kamiński
,
David B. Morse
,
Marcin Tabaka
,
Anna L. Ellermann
,
Timo N. Kohler
,
Gianluca Amadei
,
Charlotte E. Handford
,
Gregory M. Findlay
,
Magdalena Zernicka‐Goetz
,
Sarah A. Teichmann
,
Florian Hollfelder
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.01.12.523500
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.01.12.523500
Droplet microfluidic methods have massively increased the throughput of single-cell sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples and the overall RNA capture efficiency is lower. These drawbacks stem from the lack of strategies to enrich for high-quality material or specific cell types at the moment of cell encapsulation and the absence of implementable multi-step enzymatic processes that increase capture. Here we alleviate both bottlenecks using fluorescence-activated droplet sorting to enrich for droplets that contain single viable cells, intact nuclei, fixed cells or target cell types and use reagent addition to droplets by picoinjection to perform multi-step lysis and reverse transcription. Our methodology increases gene detection rates fivefold, while reducing background noise by up to half. We harness these unique properties to deliver a high-quality molecular atlas of mouse brain development, despite starting with highly damaged input material, and provide an atlas of nascent RNA transcription during mouse organogenesis. Our method is broadly applicable to other droplet-based workflows to deliver sensitive and accurate single-cell profiling at a reduced cost.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2023.01.12.523500
- https://www.biorxiv.org/content/biorxiv/early/2023/01/13/2023.01.12.523500.full.pdf
- OA Status
- green
- Cited By
- 2
- References
- 68
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4316020640
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4316020640Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2023.01.12.523500Digital Object Identifier
- Title
-
spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information contentWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-01-13Full publication date if available
- Authors
-
Joachim De Jonghe, Tomasz S. Kamiński, David B. Morse, Marcin Tabaka, Anna L. Ellermann, Timo N. Kohler, Gianluca Amadei, Charlotte E. Handford, Gregory M. Findlay, Magdalena Zernicka‐Goetz, Sarah A. Teichmann, Florian HollfelderList of authors in order
- Landing page
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https://doi.org/10.1101/2023.01.12.523500Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2023/01/13/2023.01.12.523500.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2023/01/13/2023.01.12.523500.full.pdfDirect OA link when available
- Concepts
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Microfluidics, Workflow, RNA, Nanotechnology, Cell, Single-cell analysis, Computational biology, Computer science, Massively parallel, Lysis, Chemistry, Cell biology, Biology, Biological system, Materials science, Gene, Molecular biology, Biochemistry, Parallel computing, DatabaseTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
2Total citation count in OpenAlex
- Citations by year (recent)
-
2023: 2Per-year citation counts (last 5 years)
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68Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.processes | 66 |
| abstract_inverted_index.profiling | 174 |
| abstract_inverted_index.sensitive | 170 |
| abstract_inverted_index.workflows | 167 |
| abstract_inverted_index.applicable | 163 |
| abstract_inverted_index.background | 22, 120 |
| abstract_inverted_index.campaigns. | 12 |
| abstract_inverted_index.efficiency | 33 |
| abstract_inverted_index.multi-step | 64, 106 |
| abstract_inverted_index.processing | 25 |
| abstract_inverted_index.properties | 130 |
| abstract_inverted_index.sequencing | 11 |
| abstract_inverted_index.strategies | 43 |
| abstract_inverted_index.throughput | 8 |
| abstract_inverted_index.accompanied | 19 |
| abstract_inverted_index.bottlenecks | 74 |
| abstract_inverted_index.challenging | 26 |
| abstract_inverted_index.methodology | 112 |
| abstract_inverted_index.single-cell | 10, 173 |
| abstract_inverted_index.development, | 140 |
| abstract_inverted_index.high-quality | 47, 134 |
| abstract_inverted_index.microfluidic | 2 |
| abstract_inverted_index.droplet-based | 166 |
| abstract_inverted_index.encapsulation | 58 |
| abstract_inverted_index.implementable | 63 |
| abstract_inverted_index.picoinjection | 103 |
| abstract_inverted_index.transcription | 155 |
| abstract_inverted_index.organogenesis. | 158 |
| abstract_inverted_index.transcription. | 110 |
| abstract_inverted_index.fluorescence-activated | 76 |
| cited_by_percentile_year.max | 96 |
| cited_by_percentile_year.min | 94 |
| corresponding_author_ids | https://openalex.org/A5051612157 |
| countries_distinct_count | 3 |
| institutions_distinct_count | 12 |
| corresponding_institution_ids | https://openalex.org/I241749 |
| citation_normalized_percentile.value | 0.63175717 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |