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An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq

Recent developments have enabled rapid, inexpensive RNA sequencing of thousands of individual cells from a single specimen, raising the possibility of unbiased and comprehensive expression profiling from complex tissues. Microwell arrays are a particularly attractive microfluidic platform for single...

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Detalles Bibliográficos
Autores principales: Yuan, Jinzhou, Sims, Peter A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5037380/
https://www.ncbi.nlm.nih.gov/pubmed/27670648
http://dx.doi.org/10.1038/srep33883
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author Yuan, Jinzhou
Sims, Peter A.
author_facet Yuan, Jinzhou
Sims, Peter A.
author_sort Yuan, Jinzhou
collection PubMed
description Recent developments have enabled rapid, inexpensive RNA sequencing of thousands of individual cells from a single specimen, raising the possibility of unbiased and comprehensive expression profiling from complex tissues. Microwell arrays are a particularly attractive microfluidic platform for single cell analysis due to their scalability, cell capture efficiency, and compatibility with imaging. We report an automated microwell array platform for single cell RNA-Seq with significantly improved performance over previous implementations. We demonstrate cell capture efficiencies of >50%, compatibility with commercially available barcoded mRNA capture beads, and parallel expression profiling from thousands of individual cells. We evaluate the level of cross-contamination in our platform by both tracking fluorescent cell lysate in sealed microwells and with a human-mouse mixed species RNA-Seq experiment. Finally, we apply our system to comprehensively assess heterogeneity in gene expression of patient-derived glioma neurospheres and uncover subpopulations similar to those observed in human glioma tissue.
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spelling pubmed-50373802016-09-30 An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq Yuan, Jinzhou Sims, Peter A. Sci Rep Article Recent developments have enabled rapid, inexpensive RNA sequencing of thousands of individual cells from a single specimen, raising the possibility of unbiased and comprehensive expression profiling from complex tissues. Microwell arrays are a particularly attractive microfluidic platform for single cell analysis due to their scalability, cell capture efficiency, and compatibility with imaging. We report an automated microwell array platform for single cell RNA-Seq with significantly improved performance over previous implementations. We demonstrate cell capture efficiencies of >50%, compatibility with commercially available barcoded mRNA capture beads, and parallel expression profiling from thousands of individual cells. We evaluate the level of cross-contamination in our platform by both tracking fluorescent cell lysate in sealed microwells and with a human-mouse mixed species RNA-Seq experiment. Finally, we apply our system to comprehensively assess heterogeneity in gene expression of patient-derived glioma neurospheres and uncover subpopulations similar to those observed in human glioma tissue. Nature Publishing Group 2016-09-27 /pmc/articles/PMC5037380/ /pubmed/27670648 http://dx.doi.org/10.1038/srep33883 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Yuan, Jinzhou
Sims, Peter A.
An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq
title An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq
title_full An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq
title_fullStr An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq
title_full_unstemmed An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq
title_short An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq
title_sort automated microwell platform for large-scale single cell rna-seq
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5037380/
https://www.ncbi.nlm.nih.gov/pubmed/27670648
http://dx.doi.org/10.1038/srep33883
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