Single-Cell and Ultra-Low-Input RNA-Seq
Introduction to Single-Cell RNA Sequencing
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.
Highly sensitive ultra-low-input and single-cell RNA sequencing (RNA-Seq) methods enable researchers to explore the distinct biology of individual cells in complex tissues and understand cellular subpopulation responses to environmental cues. These assays enhance the study of cell function and heterogeneity in time-dependent processes such as differentiation, proliferation, and tumorigenesis.
Advantages of Single-Cell RNA-Seq
Single-cell and ultra-low-input RNA-Seq are powerful tools for studying the transcriptome in an unbiased manner from minimal input.
- Robust transcriptome analysis down to single-cell input levels for high-quality samples
- Integrated protocol proceeds directly from whole cells and preserves sample integrity
- High resolution analysis enables discovery of cellular differences usually masked by bulk sampling methods
Single-Cell Sequencing and Analysis Workflow Video
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.
Single-Cell Sequencing Approaches
Quality Control for Single-Cell Sequencing Experiments
Learn best practices for preparing cell suspensions with sample preparation solutions from Miltenyi Biotec.
View WebinarEmpowering Single-Cell Experiments with Multiplexing
Researchers from UCSF discuss MULTI-Seq, a sample barcoding strategy for single-cell and single-nucleus RNA sequencing.
View WebinarCombinatorial Single-Cell Technologies
We highlight several applications of fully supported workflows that can take you from single-cell suspensions to analyzed data.
View WebinarDRAGEN now features a Single-Cell RNA Pipeline
The DRAGEN Single-Cell RNA offers a cell x gene expression matrix output starting point for downstream single cell analysis.
Key features include:
- Ultra-rapid. Analysis times less than 40 minutes for ~8000 cells with > 1 billion reads**
- Widely compatible: Supports a wide range of input library types, giving a common output of cell x gene expression matrix compatible with downstream analysis tools
- Efficient: Goes from BCL files to quantified expression per cell with a single tool
Single-Cell RNA-Seq is Advancing Insights in Developmental Biology
Cole Trapnell, PhD, is the principal developer of TopHat, Cufflinks, and other widely used bioinformatics tools. He shared with us his views on the importance of understanding cell lineage, his lab's experience with single-cell RNA sequencing, and his application of combinatorial indexing.
Read InterviewSingle-Cell RNA Sequencing Applications
Single-Cell Gene Expression + ATAC-Seq with 10x Genomics
Unify single-cell gene expression and chromatin accessibility to help reveal cellular mechanisms driving gene regulation.
Exploring transcriptome with single-cell resolution
Enabling research to tease apart cellular heterogeneity in complex samples using Chromium Single Cell Gene Expression from 10x Genomics
Correlating the expression of protein and RNA
Learn more about single-cell sequencing technologies that combine analysis of RNA and protein with BioLegend
Considerations, Trends and Future of Single-Cell Sequencing
From Crohn's disease and peanut allergies to cell therapies and immunotherapies, the lab at NIHR Guys' and St. Thomas' Biomedical Research Centre is using Illumina technology for single-cell genomics investigations.
Single-Cell Sequencing Research Articles
The Weizmann Institute Uses NovaSeq for Single-Cell Research
By analyzing one cell at a time, Professor Amit is improving our understanding of biological systems in health and disease.
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Exploring the Tumor Microenvironment
Single-cell sequencing proves invaluable in detecting intracellular communication in tumors.
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Single-Cell Research Review
See an overview of peer-reviewed publications using Illumina technology for single-cell sequencing.
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Single-Cell RNA Sequencing in Immunotherapy Research
Swetha Anandhan from the MD Anderson Cancer Center joins Illumina and 10x Genomics for this webinar. She highlights the use of single cell RNA-sequencing to identify a unique population of macrophages in glioblastoma multiforme that persists after treatment with immune checkpoint inhibitors.
View WebinarWorkflows for RNA Sequencing Guide
In this guide, you'll learn about the robust selection of Illumina solutions for next-generation RNA sequencing applications. Illumina RNA sequencing workflows seamlessly integrate library prep, sequencing, and data analysis to support transcriptome research.
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High- and Low-Throughput Methods
Single-cell sequencing methods can be distinguished by cell throughput. Low-throughput methods include mechanical manipulation or cell sorting/partitioning technologies and are able to process dozens to a few hundred cells per experiment.
Recent advances in microfluidic technologies have enabled high-throughput single cell profiling where researchers can examine hundreds to tens of thousands of cells per experiment in a cost-effective manner. Both the high - and low- throughput methods utilize Illumina sequencing by synthesis (SBS) chemistry, an industry leading sequencing technology. Illumina SBS technology generates >90% of the world's sequencing data.*
The Singular Neuron
James Eberwine explains how single-cell RNA sequencing can be used in vivo to understand how individual cells function in their microenvironment within a complex organism.
View VideoHigh-Throughput Workflow for Ultra-Low-Input and Single-Cell RNA-Seq
Gain valuable insight into gene expression with this sensitive, scalable, and cost-effective high-throughput workflow.
iSeq 100 System and Reagents
The iSeq 100 Sequencing System makes next-generation sequencing easier and more affordable than ever. Designed for simplicity, it allows labs of all sizes to sequence DNA and RNA at the push of a button.
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NovaSeq Reagent Kits
Reagent kits for the NovaSeq 6000 System provide ready-to-use cartridge-based reagents for cluster generation and SBS.
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NextSeq 1000 & 2000 Systems
These cost-efficient, user-friendly, mid-throughput benchtop sequencers offer extreme flexibility to support new and emerging applications.
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Nextera XT and Nextera DNA Flex
Prepare sequencing libraries for small genomes, amplicons, plasmids, and other applications.
View ProductLow-Throughput Workflow for Ultra-Low-Input and Single-Cell RNA-Seq
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.
Related Solutions
Choosing an NGS Company
Seek out a best-in-class next-generation sequencing company with user-friendly bioinformatics tools and industry-leading support and service.
See the Evidence
Protein Detection by Sequencing
Methods that allow researchers to simultaneously sequence RNA and detect extracellular proteins in individual cells reveal new cell types and states associated with disease.
Read More
ATAC Sequencing
ATAC-Seq is a widely used method that uses the hyperactive transposase Tn5 to assess chromatin accessibility. It can be performed on single cells at high resolution.
Learn more about ATAC-Seq
Cancer RNA Sequencing
Detect cancer gene expression and transcriptome changes and identify novel cancer transcripts with RNA-Seq.
Learn More
Cellular and Molecular Biology
NGS methods help broaden research beyond conventional methods and allow global analyses of gene expression and regulation.
Learn MoreFrequently Purchased Together
Featured Publications
Single-cell RNA-Seq analysis identifies cell-cell communication associated with tumor characteristics
Researchers characterized cell-to-cell communication via ligand-receptor interactions across cell types in a tumor microenvironment.
Read PublicationHuman haematopoietic stem cell lineage commitment is a continuous process
Scientists used single-cell RNA sequencing to demonstrate that hematopoietic stem cell lineage commitment is a gradual process without differentiation into discrete progenitors.
Read PublicationAging increases cell-to-cell transcriptional variability upon immune stimulation
Researchers used single-cell RNA-Seq to explore the effects of aging on the immune system, observing that age-related cell-to-cell transcriptional variability is a hallmark of aging.
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Additional Resources
Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells
Gain insight into how individual cells contribute to the function of a complex tissue such as peripheral blood.
Stem Cell Research with Single-Cell RNA-Seq
See how single-cell sequencing is transforming our view of cellular development in stem cells.
Single-Cell RNA-Seq, the Internet, and Memory
TGen researchers use single-cell RNA sequencing to understand how individual neurons are involved in memory formation.
Spotlight on Single-Cell Transcriptomics
Learn about the emerging applications of single-cell RNA sequencing and the expanding portfolio of Illumina solutions supporting single-cell research.
*Data calculations on file. Illumina, Inc., 2015
**Data calculations on file. Illumina, Inc., 2020
**Data calculations on file. Illumina, Inc., 2020