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Microfluidics-free single-cell genomics with templated emulsification
Current single-cell RNA-sequencing approaches have limitations that stem from the microfluidic devices or fluid handling steps required for sample processing. We develop a method that does not require specialized microfluidic devices, expertise or hardware. Our approach is based on particle-template...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group US
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10635830/ https://www.ncbi.nlm.nih.gov/pubmed/36879006 http://dx.doi.org/10.1038/s41587-023-01685-z |
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author | Clark, Iain C. Fontanez, Kristina M. Meltzer, Robert H. Xue, Yi Hayford, Corey May-Zhang, Aaron D’Amato, Chris Osman, Ahmad Zhang, Jesse Q. Hettige, Pabodha Ishibashi, Jacob S. A. Delley, Cyrille L. Weisgerber, Daniel W. Replogle, Joseph M. Jost, Marco Phong, Kiet T. Kennedy, Vanessa E. Peretz, Cheryl A. C. Kim, Esther A. Song, Siyou Karlon, William Weissman, Jonathan S. Smith, Catherine C. Gartner, Zev J. Abate, Adam R. |
author_facet | Clark, Iain C. Fontanez, Kristina M. Meltzer, Robert H. Xue, Yi Hayford, Corey May-Zhang, Aaron D’Amato, Chris Osman, Ahmad Zhang, Jesse Q. Hettige, Pabodha Ishibashi, Jacob S. A. Delley, Cyrille L. Weisgerber, Daniel W. Replogle, Joseph M. Jost, Marco Phong, Kiet T. Kennedy, Vanessa E. Peretz, Cheryl A. C. Kim, Esther A. Song, Siyou Karlon, William Weissman, Jonathan S. Smith, Catherine C. Gartner, Zev J. Abate, Adam R. |
author_sort | Clark, Iain C. |
collection | PubMed |
description | Current single-cell RNA-sequencing approaches have limitations that stem from the microfluidic devices or fluid handling steps required for sample processing. We develop a method that does not require specialized microfluidic devices, expertise or hardware. Our approach is based on particle-templated emulsification, which allows single-cell encapsulation and barcoding of cDNA in uniform droplet emulsions with only a vortexer. Particle-templated instant partition sequencing (PIP-seq) accommodates a wide range of emulsification formats, including microwell plates and large-volume conical tubes, enabling thousands of samples or millions of cells to be processed in minutes. We demonstrate that PIP-seq produces high-purity transcriptomes in mouse–human mixing studies, is compatible with multiomics measurements and can accurately characterize cell types in human breast tissue compared to a commercial microfluidic platform. Single-cell transcriptional profiling of mixed phenotype acute leukemia using PIP-seq reveals the emergence of heterogeneity within chemotherapy-resistant cell subsets that were hidden by standard immunophenotyping. PIP-seq is a simple, flexible and scalable next-generation workflow that extends single-cell sequencing to new applications. |
format | Online Article Text |
id | pubmed-10635830 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group US |
record_format | MEDLINE/PubMed |
spelling | pubmed-106358302023-11-15 Microfluidics-free single-cell genomics with templated emulsification Clark, Iain C. Fontanez, Kristina M. Meltzer, Robert H. Xue, Yi Hayford, Corey May-Zhang, Aaron D’Amato, Chris Osman, Ahmad Zhang, Jesse Q. Hettige, Pabodha Ishibashi, Jacob S. A. Delley, Cyrille L. Weisgerber, Daniel W. Replogle, Joseph M. Jost, Marco Phong, Kiet T. Kennedy, Vanessa E. Peretz, Cheryl A. C. Kim, Esther A. Song, Siyou Karlon, William Weissman, Jonathan S. Smith, Catherine C. Gartner, Zev J. Abate, Adam R. Nat Biotechnol Article Current single-cell RNA-sequencing approaches have limitations that stem from the microfluidic devices or fluid handling steps required for sample processing. We develop a method that does not require specialized microfluidic devices, expertise or hardware. Our approach is based on particle-templated emulsification, which allows single-cell encapsulation and barcoding of cDNA in uniform droplet emulsions with only a vortexer. Particle-templated instant partition sequencing (PIP-seq) accommodates a wide range of emulsification formats, including microwell plates and large-volume conical tubes, enabling thousands of samples or millions of cells to be processed in minutes. We demonstrate that PIP-seq produces high-purity transcriptomes in mouse–human mixing studies, is compatible with multiomics measurements and can accurately characterize cell types in human breast tissue compared to a commercial microfluidic platform. Single-cell transcriptional profiling of mixed phenotype acute leukemia using PIP-seq reveals the emergence of heterogeneity within chemotherapy-resistant cell subsets that were hidden by standard immunophenotyping. PIP-seq is a simple, flexible and scalable next-generation workflow that extends single-cell sequencing to new applications. Nature Publishing Group US 2023-03-06 2023 /pmc/articles/PMC10635830/ /pubmed/36879006 http://dx.doi.org/10.1038/s41587-023-01685-z Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Clark, Iain C. Fontanez, Kristina M. Meltzer, Robert H. Xue, Yi Hayford, Corey May-Zhang, Aaron D’Amato, Chris Osman, Ahmad Zhang, Jesse Q. Hettige, Pabodha Ishibashi, Jacob S. A. Delley, Cyrille L. Weisgerber, Daniel W. Replogle, Joseph M. Jost, Marco Phong, Kiet T. Kennedy, Vanessa E. Peretz, Cheryl A. C. Kim, Esther A. Song, Siyou Karlon, William Weissman, Jonathan S. Smith, Catherine C. Gartner, Zev J. Abate, Adam R. Microfluidics-free single-cell genomics with templated emulsification |
title | Microfluidics-free single-cell genomics with templated emulsification |
title_full | Microfluidics-free single-cell genomics with templated emulsification |
title_fullStr | Microfluidics-free single-cell genomics with templated emulsification |
title_full_unstemmed | Microfluidics-free single-cell genomics with templated emulsification |
title_short | Microfluidics-free single-cell genomics with templated emulsification |
title_sort | microfluidics-free single-cell genomics with templated emulsification |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10635830/ https://www.ncbi.nlm.nih.gov/pubmed/36879006 http://dx.doi.org/10.1038/s41587-023-01685-z |
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