Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation
Year: 2020
Type: article
Abstract: A comprehensive reference map of all cell types in the human body is necessary for improving our understanding of fundamental biological processes and in diagnosing and treating disease. High-throughput single-cell RNA sequencing techniques have emerged as powerful tools to identify and characterize cell types in complex and heterogeneous tissues. However, extracting intact cells from tissues and organs is often technically challenging or impossible, for example in heart or brain tissue. Single-nucleus RNA sequencing provides an alternative way to obtain transcriptome profiles of such tissues. To systematically assess the differences between high-throughput single-cell and single-nuclei RNA-seq approaches, we compared Drop-seq and DroNc-seq, two microfluidic-based 3' RNA capture technologies that profile total cellular and nuclear RNA, respectively, during a time course experiment of human induced pluripotent stem cells (iPSCs) differentiating into cardiomyocytes. Clustering of time-series transcriptomes from Drop-seq and DroNc-seq revealed six distinct cell types, five of which were found in both techniques. Furthermore, single-cell trajectories reconstructed from both techniques reproduced expected differentiation dynamics. We then applied DroNc-seq to postmortem heart tissue to test its performance on heterogeneous human tissue samples. Our data confirm that DroNc-seq yields similar results to Drop-seq on matched samples and can be successfully used to generate reference maps for the human cell atlas.
Source: Scientific Reports
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,870
Funders: U.S. Department of Energy, U.S. Department of Health and Human Services, American Heart Association, University of Chicago, Chan Zuckerberg Initiative, National Institutes of Health, Office of Science, National Heart, Lung, and Blood Institute, National Institute of General Medical Sciences, National Institute of Biomedical Imaging and Bioengineering, National Center for Advancing Translational Sciences
Awards: G102163711, G1055550527, G1298244684, G1505794299, Graduate Program in Biophysical Sciences at the University of Chicago, G2101401529, G2248975092, G2287611682, G2289426772, G262962599, Medical Scientist National Research Service Award, G3277895032, G498139845, G5106849484, Mapping Functional Variation in Gene Regulatory Dynamics in Human Cardiomyocytes, G5607048534, Training of Junior Faculty for Careers in Omics of Lung Diseases, G6848031779, G6918803902, Genetics and Regulation, G7368700025, G969889393, G993149817
OpenAlex ID: W3003421376