Single-cell sequencing-based technologies will revolutionize whole-organism science

  title={Single-cell sequencing-based technologies will revolutionize whole-organism science},
  author={Ehud Y. Shapiro and Tamir Biezuner and Sten Linnarsson},
  journal={Nature Reviews Genetics},
The unabated progress in next-generation sequencing technologies is fostering a wave of new genomics, epigenomics, transcriptomics and proteomics technologies. These sequencing-based technologies are increasingly being targeted to individual cells, which will allow many new and longstanding questions to be addressed. For example, single-cell genomics will help to uncover cell lineage relationships; single-cell transcriptomics will supplant the coarse notion of marker-based cell types; and… 

Single-cell RNA-sequencing: The future of genome biology is now

Genome-wide single-cell analysis represents the ultimate frontier of genomics research and will have a profound impact in many aspects of society, from the introduction of truly tailored cancer treatments, to a better understanding of antibiotic resistance and host-pathogen interactions.

Gene Expression Analysis of T-Cells by Single-Cell RNA-Seq.

An optimized protocol for the isolation of T cells and the preparation of RNA sequencing libraries by using droplet digital technology (ddSEQ, Bio-Rad Laboratories) is provided, which will support users in building a single-cell experimental framework.

Single-Cell Omics: An Overview

Single-Cell Applications of Next-Generation Sequencing.

The goal of this article is to provide a high-level overview of single-cell sequencing for the nonexpert and show how its applications are influencing both basic and applied clinical studies in embryology, developmental genetics, and cancer.

Single-cell genome sequencing: current state of the science

An overview of the current state of the field of single-cell genome sequencing is provided, focusing on the technical challenges of making measurements that start from a single molecule of DNA, and how some of these recent methodological advancements have enabled the discovery of unexpected new biology.

Single-cell sequencing technologies: current and future.

Single-Cell Genomic Analysis in Plants

The technical challenges of analysing material from a single plant cell are outlined, the applications of single-cell genomics are examined, and the integration of this approach with genome editing is examined.

Single-Cell Transcriptional Analysis.

This review provides a broad introduction to this revolutionary technology by presenting the state-of-the-art in sample preparation methodologies, technology platforms, and computational analysis methods, while highlighting the key considerations for designing, executing, and interpreting a study using single-cell RNA sequencing.

Technology: Bead capture for single-cell transcriptomics

A bead-based approach to characterize a custom subset of the transcriptome across thousands of cells, offering a complementary method that is scalable to a large number of samples and potentially limiting the ability to discover roles for genes that are not known to be involved in the process under study.

Single-Cell Genomics and Epigenomics

This chapter reviews the major technological developments achieved in single cell “omics” as well as the technical challenges to overcome and the potential of future developments, and describes the impact that these methods would have on normal development and disease and their potential applications.



Perspectives and challenges of emerging single-molecule DNA sequencing technologies.

The growing demand for analysis of the genomes of many species and cancers, for understanding the role of genetic variation among individuals in disease, and with the ultimate goal of deciphering

The future is now: single-cell genomics of bacteria and archaea.

Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology.

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.

This strategy will enable the unbiased discovery and analysis of naturally occurring cell types during development, adult physiology, and disease and be demonstrated by analyzing the transcriptomes of 85 single cells of two distinct types.

A window into third-generation sequencing.

A new generation of single-molecule sequencing technologies (third-generation sequencing) that is emerging to fill this space, with the potential for dramatically longer read lengths, shorter time to result and lower overall cost.

Exome sequencing: the sweet spot before whole genomes

Some of the methodologies currently used for genomic and exome capture are described and recent applications of this technology are highlighted.

Accurate whole genome sequencing and haplotyping from10-20 human cells

A low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes is described.

mRNA-Seq whole-transcriptome analysis of a single cell

A single-cell digital gene expression profiling assay with only a single mouse blastomere is described, which detected the expression of 75% more genes than microarray techniques and identified 1,753 previously unknown splice junctions called by at least 5 reads.

High-throughput microfluidic single-cell RT-qPCR

This work presents a fully integrated microfluidic device capable of performing high-precision RT-qPCR measurements of gene expression from hundreds of single cells per run, and shows that nanoliter volume processing reduced measurement noise, increased sensitivity, and provided single nucleotide specificity.