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 sequencing
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
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 Workflow Considerations
Want to learn valuable insights about the single-cell sequencing workflow?
Single-Cell Research Review
See an overview of peer-reviewed publications using Illumina technology for single-cell sequencing.
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.
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.
Other advances have enabled high-throughput single-cell profiling where researchers can examine hundreds to millions 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.
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.
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.
Single-cell RNA data analysis and insights
DRAGEN single-cell RNA Pipeline
The DRAGEN Single-Cell RNA (scRNA) Pipeline can process multiplexed single-cell RNA-Seq data sets from reads to a cell-by-gene 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:
- RNA-Seq (splice-aware) alignment and matching to annotated genes for the transcript reads
- Cell-barcode and UMI error correction for the barcode reads
- Genotype-based and genotype-free sample demultiplexing
- UMI counting per cell and gene to measure gene expression
- Cell hashing and feature counting by read 2 UMI
- Sparse gene expression matrix output
- Single cell RNA QC metrics
Partek Flow
Partek Flow 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.
- Import your own data or publicly available data from popular online repositories
- Remove batch effects to discover biological information
- Perform pseduo bulk analysis
- Discover biomarkers that define a cell population
- Find differentially expressed genes and proteins
Single-cell RNA resources
Single-cell webinars
How to explore single-cell data
This presentation introduces the basic steps in tertiary scRNA-Seq analyses, highlighting how different cell populations can react to external factors.
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Single-cell RNA sequencing across multiple sites
New technology enables single-cell RNA sequencing from multiple sites in one workflow. This webinar covers data quality, fragile cell recovery, custom primers, and more.
Single-cell multiomics: Beyond RNA-Seq
In this webinar, Dr. Michael Kelly applies Single-cell sequencing to study auditory development and supports research at the NCI Center for Cancer Research.
Single-cell 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.
Single-Cell Gene Expression + ATAC-Seq
Unify single-cell gene expression and chromatin accessibility to help reveal cellular mechanisms driving gene regulation.
Single-cell and spatial sequencing on NextSeq 1000 and 2000 Systems
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.
Keep exploring
Cancer Single-Cell Analysis
Single-cell sequencing powered by next-generation sequencing (NGS) can examine the genomes or transcriptomes of individual cancer cells, providing a high-resolution view of cell-to-cell variation.
CITE-Seq
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.
Transcriptomics
Transcriptomics is the complete study of the transcriptome which includes all RNA molecules found within an organism. Explore various techniques to learn how the discovery power of RNA-seq can empower high-impact research.
Single-Cell Sequencing Applications
Single-Cell Sequencing Products
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 InterviewHigh- 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.*
NovaSeq Reagent Kits
Reagent kits for the NovaSeq 6000 System provide ready-to-use cartridge-based reagents for cluster generation and SBS.
View Product 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 550 System and Reagents
The NextSeq 550 System brings the power of a high-throughput sequencing system to your benchtop.
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 ProductRelated Solutions
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. Learn more about single-cell RNA-Seq in marine research.
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.
Single-Cell Interviews and Publications
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.
Read PublicationHuman 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.
Read PublicationAging increases cell-to-cell transcriptional variability upon immune stimulation
AResearchers 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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