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

Highly sensitive RNA sequencing (RNA-Seq) methods now enable gene expression analysis of very low-input samples and even single cells. Ultra-low-input and single-cell RNA-Seq offer higher resolution to discover cellular differences usually masked by bulk sampling methods.

Single-cell RNA-Seq lets you read the gene expression of one individual cell at a time. With these sensitive assays, you can explore the distinct biology of different cells within an organ or a tumor, and understand subpopulation responses to environmental cues.

Sample Prep for Ultra-Low-Input and Single-Cell RNA-Seq

cDNA Synthesis

The SMARTer® Ultra™ Low Input RNA Kit, sold and supported by Clontech, is a cDNA synthesis kit designed for single-cell or ultra-low-input RNA-Seq. The kit enables robust transcriptome analysis down to single-cell input levels in high-quality samples, and is optimized for Illumina sequencing.

The assay accurately synthesizes full-length cDNA from only 1-1000 whole cells or 10 pg-10 ng high-quality total RNA. The single-tube protocol works directly on whole cells and preserves sample integrity.

Library Preparation

The Nextera XT DNA Library Preparation Kit is optimal for preparing an Illumina RNA sequencing library from cDNA generated with the Clontech SMARTer Ultra Low Input RNA kit.

Our selection tool can help you choose the right RNA-Seq library prep kit for your needs:

Product Selector
Find the right kit »

Data Analysis Solutions for Single-Cell and Ultra-Low-Input RNA-Seq

Visit the RNA-Seq Data Analysis page to find user-friendly apps for analysis of RNA sequencing data.  

Review of Single Cell Research

This document highlights publications using Illumina technology for single-cell sequencing and very low input applications and techniques.

Read Review (PDF) »

Single-Cell RNA-Seq in Action

Learn how stem cell researchers are using RNA-Seq with the NextSeq 500 system to study gene expression in single cells.

Read Article (PDF) »

Illumina Sequencing Systems


Find the NGS system that’s right for your lab.

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Push-Button Informatics

Our user-friendly BaseSpace genomics computing environment offers simple analysis and sharing of NGS data.

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