单细胞转录组分析

Q1 Agricultural and Biological Sciences Current protocols in mouse biology Pub Date : 2017-09-08 DOI:10.1002/cpmo.30

Wanze Chen, Vincent Gardeux, Antonio Meireles-Filho, Bart Deplancke

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引用次数: 10

摘要

复杂的生物系统是由多种细胞类型组成的，它们的转录活性会因细胞状态、环境刺激或内在程序的差异而变化。传统的批量分析方法捕获细胞群体的平均转录程序，因此错过了每个单细胞的独特细胞特征。近年来，单细胞rna测序(scRNA-seq)技术的发展为解剖复杂生物系统的细胞异质性提供了强有力的方法。然而，这种方法需要专门的设备或费用昂贵。在本文中，我们描述了一种改进的基于smart -seq2的方法，可以同时分析数百个单细胞的转录组，而不需要使用商业试剂盒或任何专门的单细胞捕获/文库制备工具。此外，我们还介绍了自动化单细胞分析管道(ASAP)，它允许没有强大计算专业知识的研究人员使用广泛的常用算法和复杂的可视化工具来探索scRNA-seq数据。©2017 by John Wiley &儿子,Inc。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Profiling of Single-Cell Transcriptomes

Complex biological systems are composed of multiple cell types whose transcriptional activity can vary due to differences in cell state, environmental stimulation, or intrinsic programs. Conventional bulk analysis methods capture the average transcriptional programs of the cell population, thus missing the unique cellular signature of each single cell. In recent years, the development of single-cell RNA-sequencing (scRNA-seq) technologies has provided a powerful approach to dissect the cellular heterogeneity of complex biological systems. However, such approaches require specialized equipment or are costly. In this article, we describe an improved Smart-seq2-based method to profile the transcriptome of hundreds of single cells simultaneously, without utilizing commercial kits or requiring any specialized single-cell capture/library preparation tools. Moreover, we introduce the Automated Single-cell Analysis Pipeline (ASAP), which allows researchers without strong computational expertise to explore scRNA-seq data using a wide range of commonly used algorithms and sophisticated visualization tools. © 2017 by John Wiley & Sons, Inc.

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Current protocols in mouse biology Agricultural and Biological Sciences-Animal Science and Zoology

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期刊介绍： Sound and reproducible laboratory methods are the foundation of scientific discovery. Yet, all too often, nuances that are critical for an experiment''s success are not captured in the primary literature but exist only as part of a lab''s oral tradition. The aim of Current Protocols in Mouse Biology is to provide the clearest, most detailed and reliable step-by-step instructions for protocols involving the use of mice in biomedical research. Written by experts in the field and extensively edited to our exacting standards, the protocols include all of the information necessary to complete an experiment in the laboratory—introduction, materials lists with supplier information, detailed step-by-step procedures with helpful annotations, recipes for reagents and solutions, illustrative figures and information-packed tables. Each article also provides invaluable discussions of background information, applications of the methods, important assumptions, key parameters, time considerations, and tips to help avoid common pitfalls and troubleshoot experiments. Furthermore, Current Protocols in Mouse Biology content is thoughtfully organized by topic for optimal usage and to maximize contextual knowledge. Quarterly issues allow Current Protocols to constantly evolve to keep pace with the newest discoveries and developments. Current Protocols in Mouse Biology brings together resources in mouse biology and genetics and provides a mouse protocol resource that covers all aspects of mouse biology. Current Protocols in Mouse Biology also permits optimization of mouse model usage, which is significantly impacted by both cost and ethical constraints. Optimal and standardized mouse protocols ultimately reduce experimental variability and reduce the number of animals used in mouse experiments.