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Single-Cell and Ultra-Low-Input RNA-Seq

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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

Single-Cell Sequencing Virtual Symposium

Join us for one or several of our 10 free virtual events, co-hosted with our partners. You'll gain insight from some of the greatest minds in single-cell multimodal omics. Explore emerging techniques and protocols, visit our virtual exhibit hall, and chat with other attendees.

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Single-Cell Sequencing and Analysis Workflow

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.

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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

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Empowering Single-Cell Experiments with Multiplexing

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

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Combinatorial Single-Cell Technologies

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

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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.

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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

Considerations, Trends and Future of Single-Cell Sequencing

From Crohn's disease and peanut alergies 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
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.

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Buyer’s Guide to Simple RNA-Seq Workflows

RNA-Seq offers many advantages over previous methods such as qPCR and gene expression arrays. Evaluate options for next-generation sequencing and get customized workflows with this guide.

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Buyer’s Guide to Simple RNA-Seq Workflows

Single-Cell Sequencing Applications

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.

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Single-Cell Sequencing on the NovaSeq 6000 System

This scalable, robust, single-cell NGS methodology enables routine transcriptome profiling at single-cell resolution.

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For All You Seq Single-Cell Technology Poster
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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, the most widely adopted NGS technology, which generates approximately 90% of sequencing data worldwide.*

High-Throughput Workflow for Ultra-Low-Input and Single-Cell RNA-Seq

The Illumina Bio-Rad Single-Cell RNA Sequencing Solution combines the highly innovative Bio-Rad Droplet Digital™ technology (ddSEQ™) with Illumina NGS library preparation, sequencing, and analysis technologies. Gain valuable insight into gene expression with this sensitive, scalable, and cost-effective high-throughput workflow.

The NextSeq 1000 and NextSeq 2000 Sequencing Systems are groundbreaking benchtop sequencers that allow you to explore new science across a variety of current and emerging applications, with higher efficiency and fewer restraints.

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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 »

NovaSeq 6000 Sequencing System

The NovaSeq 6000 System combines benchtop sequencer ease of use with production-scale power in a single platform, with adjustable data output for maximum efficiency. Learn more »

Nextera XT and Nextera DNA Flex

Optimal for preparing an Illumina RNA sequencing library from cDNA generated with the SMART-Seq Ultra Low Input RNA kit. View Product »


An overview of the Illumina Single-cell sequencing and analysis workflow

Single-cell sequencing can reveal the cell types present and how individual cells are contributing to the function of that system. Learn how insights gained from single-cell NGS are within your reach.

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Considerations, trends and future of single-cell sequencing

Hear from Dr. Alka Saxena, head of the Genomics Research Platform and the Single Cell Laboratory at the NIHR Guy’s and St. Thomas’s Biomedical Research Centre.

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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.

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Frequently Purchased Together

Single-Cell Podcasts

Single-Cell Genomics and Mars

Microbes have been around for billions of years, and they continue to shape our planet and all life on it. Dr. Ramunas Stepanasukas of the Bigelow Laboratory for Ocean Sciences explains how single-cell genomics can help us to better understand microbial diversity and microbial biology. He even discuss how single-cell genomics can help us in our exploration of other planets, like Mars.

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Single Cell Genomics and Cell Ontology

Cell ontology is the vocabulary for defining cell types, and it's important in biology. Single-cell genomics is revolutionizing cell ontology but combining large data sets with classical knowledge is challenging. Dr. Richard Scheuermann, La Jolla Campus Director at the Venter Institute, discusses single-cell sequencing and computational methods to classify cell types.

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Genomics of Endosymbiosis and Cells Within Cells

Eukaryotic cells and their membrane bound organelles evolved from the uptake of a prokaryotic cell into another cell - a process called endosymbiosis. Professors Bebashish Bhattacharya and Dana Price of Rutgers University discuss how single-cell genomics of algae can help unravel the mystery of endosymbiosis and its impact on our health and the environment.

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Single-Cell Interviews and Publications

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.

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Human haematopoietic stem cell lineage commitment is a continuous process

Researchers used single-cell RNA-Seq to demonstrate that hematopoietic stem cell lineage commitment is a gradual process without differentiation into discrete progenitors.

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Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

Researchers used single-cell RNA-Seq to characterize cell-to-cell communication via ligand-receptor interactions across cell types in a tumor microenvironment.

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Single-Cell Analysis is Advancing Insights in Developmental Biology

A computer scientist transforms the world of biology by making bioinformatics tools available to all.

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Stem Cell Research with Single-Cell RNA-Seq

See how single-cell sequencing is transforming our view of cellular development in stem cells.

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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.

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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.

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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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Marine Biology: Uncover Hidden Diversity

Researchers at Bigelow Laboratory for Ocean Sciences use single-cell RNA sequencing to study bacteria inhabiting the surface layers of the ocean.

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Other Resources

RNA-Seq Data Analysis

User-friendly software tools simplify RNA-Seq data analysis for biologists, regardless of bioinformatics experience. Learn more about single-cell RNA-Seq Data Analysis.

RNA-Seq for Cancer Research

Evaluating transcriptome profile differences within tumor regions can enhance researchers' understanding of relapse and metastasis. Learn more about cancer RNA-Seq.

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.

*Data calculations on file. Illumina, Inc., 2015