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.

Want to learn valuable insights about the single-cell sequencing
    workflow? Download eBook

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.

Launch Modal

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 Webinar
Empowering Single-Cell Experiments with Multiplexing

Researchers from UCSF discuss MULTI-Seq, a sample barcoding strategy for single-cell and single-nucleus RNA sequencing.

View Webinar
Combinatorial Single-Cell Technologies

We highlight several applications of fully supported workflows that can take you from single-cell suspensions to analyzed data.

View Webinar

Single-Cell RNA Data Analysis

The DRAGEN Bio-IT Platform now features a single-cell RNA pipeline that offers a cell-by-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-by-gene-expression matrix compatible with downstream analysis tools
  • Efficient: Goes from BCL files to quantified expression per cell with a single tool
Read Blog Post
Want to learn valuable insights about the single-cell sequencing
        workflow? Download eBook

Single-Cell Analysis is Advancing Insights in Developmental Biology

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 Interview

Single-Cell RNA Sequencing Applications

NextSeq 1000 and NextSeq 2000 single-cell RNA sequencing solution

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.

View App Note

QC and Rebalancing of Libraries on iSeq 100 System

Assess key metrics of multiplexed single-cell gene expression libraries to evaluate quality before high-depth runs.

Read Application Note
Probe the immune system at single-cell resolution

A multiomic approach to determine how the adaptive immune system functions with 10x Genomics Chromium Single Cell Immune Profiling

Read Application Note
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.

Read Application Note

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

Read Technical Note

Correlating the expression of protein and RNA

Learn more about single-cell sequencing technologies that combine analysis of RNA and protein with BioLegend

Read Application Note

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.

Considerations, Trends and Future of Single-Cell Sequencing

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.

Read Article
Exploring the Tumor Microenvironment

Single-cell sequencing proves invaluable in detecting intracellular communication in tumors.

Read Interview
Single-Cell Research Review

See an overview of peer-reviewed publications using Illumina technology for single-cell sequencing.

Read Review
Immune Profiling of Human Tumors Identifies CD73 as a Combinatorial Target in Glioblastoma

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 Webinar

Workflows 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.

Download Now
Workflows for RNA Sequencing Guide

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 Video

High-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.

Learn More
iSeq 100 System and Reagents
NovaSeq Reagent Kits
NovaSeq Reagent Kits

Reagent kits for the NovaSeq 6000 System provide ready-to-use cartridge-based reagents for cluster generation and SBS.

View Product
NextSeq 1000 & 2000 Systems

These cost-efficient, user-friendly, mid-throughput benchtop sequencers offer extreme flexibility to support new and emerging applications.

Learn More
Nextera XT and Nextera DNA Flex
Nextera XT and Nextera DNA Flex

Prepare sequencing libraries for small genomes, amplicons, plasmids, and other applications.

View Product

Low-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 More

Frequently 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 Publication
Human 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 Publication
Aging 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.

Read Publication
Interested in receiving newsletters, case studies, and information on sequencing methods? Enter your email address.

Additional Resources

Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells
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
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
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
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