Complex biological systems are determined by the coordinated functions of individual cells. Conventional methods that provide bulk genome or transcriptome data are unable to reveal the cellular heterogeneity that drives this complexity. Single-cell sequencing is a next-generation sequencing (NGS) method that examines the genomes or transcriptomes of individual cells, providing a high-resolution view of cell-to-cell variation.
Ultra-low-input and single-cell RNA sequencing (scRNA-Seq) methods enable researchers to explore the distinct biology of individual cells in complex tissues and understand cellular subpopulation responses to environmental cues. Highly sensitive scRNA-Seq approaches enhance the study of cell function and heterogeneity in time-dependent processes such as differentiation, proliferation, and tumorigenesis.
Single-cell and ultra-low-input RNA-Seq methods are powerful tools for studying the transcriptome in an unbiased manner from minimal input. Single-cell RNA sequencing can be applied across diverse research areas, with the potential to transform our understanding of cellular function in health and disease.
Single-cell sequencing can reveal the cell types present and how individual cells are contributing to the function of complex biological systems. See how you can use the Illumina workflow for single-cell sequencing, from tissue preparation through analysis.
Bulk RNA-Seq excels at providing insights into the entire tissue. It can help researchers understand the big picture and may be used as an untargeted approach for new discoveries. However, bulk RNA-Seq may fail to capture transcripts from rare but biologically relevant subpopulations, such as stem cells or circulating tumor cells. In addition, a low-expressing gene identified in bulk RNA-Seq may instead be robustly expressed in a rare cell type.
In contrast, single-cell RNA sequencing data are generated for individual cells, enabling deeper insights into the nuanced distinctions between cells within the same sample. The variation between individual cells can be immense, even when examining the same cellular subpopulation. This is especially true of the transcriptome, a more reactive and dynamic -ome compared to the relative stability of the genome and epigenome. Examining complex organs and tissues at single-cell resolution is critical to advancing our understanding of many diseases and systems.
Single-cell RNA sequencing methods can be distinguished by cell throughput. High-throughput single-cell profiling methods are recommended for researchers wishing to examine hundreds to millions of cells per experiment in a cost-effective manner.
Low-throughput methods are recommended for scientists who need to process dozens to a few hundred cells per experiment. Low-throughput approaches generally include mechanical manipulation or cell sorting/partitioning technologies.
Explore workflows for both high- and low-throughput single-cell RNA-Seq methods below. Both methods utilize proven Illumina sequencing by synthesis (SBS) chemistry. Illumina sequencing systems offer high data accuracy with flexible throughput to deliver a proven NGS solution for single-cell sequencing studies, regardless of scale.
Gain valuable insight into gene expression with this sensitive, scalable, and cost-effective high-throughput scRNA-Seq method.
The low-throughput method below is recommended for researchers who wish to process small numbers of cells for a particular study, such as dozens to a few hundred cells per experiment.
The DRAGEN Single-Cell RNA (scRNA) Pipeline can process multiplexed single-cell RNA-Seq data sets from reads to a cell-by-gene unique molecular identifier (UMI) count gene expression matrix. The pipeline is compatible with library designs that have one read in a fragment match to a transcript and the other containing a cell-barcode and UMI. The pipeline includes the following functions:
Partek Flow software takes you from raw RNA-Seq data to pathways with powerful statistics and visualizations. Seamlessly analyze data with easy-to-use workflows and interactive visualizations with no command-line experience needed. It combines the powerful statistics you trust with information-rich, interactive visualizations to take your analysis from start to finish. It’s as simple as point, click, and done.
Single-cell RNA sequencing enables a broad range of applications, allowing researchers to make significant strides in understanding complex biological systems. Examples of popular applications include:
Learn more about emerging applications of scRNA-Seq and uncover deep insights into complex cellular biology.
This presentation introduces the basic steps in tertiary scRNA-Seq analyses, highlighting how different cell populations can react to external factors.
Technology advances enable single-cell RNA-Seq from multiple sites in one workflow. Learn about data quality, recovery of fragile cell types, and more.
Dr. Michael Kelly uses single-cell sequencing methods to study auditory development and supports research at the NCI Center for Cancer Research.
This cost-effective, flexible workflow measures gene expression in single cells and offers high-resolution analysis to discover cellular differences usually masked by bulk sampling methods.
Unify single-cell gene expression and chromatin accessibility to help reveal cellular mechanisms driving gene regulation.
Learn how XLEAP-SBS chemistry combined with 10x Genomics single-cell and spatial solutions enable high-resolution genomics on the NextSeq 1000 and NextSeq 2000 Systems.
Single-cell sequencing powered by NGS can examine the genomes or transcriptomes of individual cancer cells, providing a high-resolution view of cell-to-cell variation.
CITE-Seq (cellular indexing of transcriptomes and epitopes) is a sequencing-based method that simultaneously quantifies cell surface protein and transcriptomic data within a single cell readout.
Profile the transcriptome for a better understanding of biology. Explore various techniques and learn how the discovery power of RNA-seq can empower high-impact research.
Combine data from genomics, transcriptomics, epigenetics, and proteomics to better connect genotype to phenotype.
Evaluate regions of open chromatin across the genome, in either bulk cell populations or single cells at high resolution.
Dr. Alex Swarbrick discusses the advantages of single-cell sequencing for studying tumor microenvironments in breast and prostate cancers.