Accessible Single-Cell Answers

Now available and compatible with all Illumina platforms, the Illumina 3' Single Cell RNA Prep solution brings simplicity, scalability, and affordability to your lab, to gain deeper insights into the biology and pathology of individual cells, even those missed with other isolation methods.​
PIPseq™ technology

The PIPseq™ technology relies on emulsion-based Pre-Templated Instant Partitions (PIPs) to simultaneously segregate complex cell mixtures into partitions with barcoded template particles that can be easily processed for single cell applications such as scRNA-Seq. The Illumina Single Cell 3’ RNA Prep, a Illumina single cell kit renamed from PIPseq V, eliminates the need for complex, expensive instrumentation and microfluidic consumables - making high quality single-cell analysis simple, affordable, and accessible to any researcher.

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Did You Know?

What microfluidics instruments and consumables are required to run Illumina Single Cell 3’ RNA Prep?

None!
You do not require any microfluidics instrument and reagents

What is the cell capture efficiency of Illumina Single Cell 3’ RNA Prep?

You can capture up to 85% of single cells​

 

Which Illumina platform is Illumina Single Cell 3’ RNA Prep compatible with?

It's compatible with all Illumina platforms to meet your sequencing throughput requirements

 

The Workflow

llumina Single Cell 3’ RNA Prep does not require expensive microfluidic equipment or labor-intensive protocols. You can conduct single-cell studies on your benchtop using a simple manual workflow with flexible stopping points.
Prepare cell suspension​
Cell capture in PIPs​
Lysis and mRNA capture​
cDNA​
Library prep​
Sequencing
Data analysis
ON-DEMAND WEBINAR

Introducing Illumina Single-Cell 3’ RNA Prep: More Single Cell Data, Less Equipment

Join this webinar to learn more about how PIPseq technology can be seamlessly integrated into your multi-omic studies. This webinar is suitable for experienced and novice single-cell sequencing researchers.

Attend this webinar to:

  • Get an overview of single-cell sequencing methods
  • Deep dive into PIPseq technology
  • Understand research applications available with Illumina’s end-to-end single-cell sequencing solution
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NATURE ARTICLE

Barriers fall for single-cell sequencing

A new article in Nature highlights how recent innovations, including a droplet-free method called PIPseq™, now available as the Illumina Single Cell Prep kit— are making powerful single-cell tools more accessible than ever.

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INFOGRAPHIC

Illumina Single-Cell at a glance​

Download the infographic to learn the basics of the new Illumina Single-Cell end-to-end workflow.

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Publication Highlights​ ​

Microfluidics-free single-cell genomics with templated emulsification
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This study published on Nature Biotechnology introduces PIP-seq, a simple and scalable single-cell RNA-sequencing method that eliminates the need for specialized microfluidic devices. Using particle-templated emulsification and a vortexer, it enables high-throughput single-cell encapsulation and barcoding in diverse formats, from microwell plates to large-volume tubes. PIP-seq delivers high-quality transcriptomes, supports multiomics, and reveals hidden heterogeneity in cell populations, demonstrating its potential for advancing single-cell analysis in various biological and clinical applications.​
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Publication Highlights

Intrinsic molecular identifiers enable robust molecular counting in single-cell sequencing
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PIPseq V is a refined version of the PIPseq workflow for single-cell gene expression studies, offering improved sensitivity and performance without requiring complex instruments or costly consumables. It introduces Intrinsic Molecular Identifiers (IMIs), which uniquely identify transcript copies through random fragmentation positions, eliminating biases associated with traditional Unique Molecular Identifiers (UMIs). A dynamic correction strategy ensures robust analysis across varying conditions, providing comparable biological insights to UMI-based methods while enhancing scalability and flexibility.​
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Educational resources ​to learn more

Article
A cost-effective single-cell workflow advances holistic biological views​​
Article
A cost-effective single-cell workflow advances holistic biological views​​
Genome Engineering News summarizes key Illumina Single-Cell publications and discusses dramatic reductions in workflow cost and complexity.
Video
Scalable single-cell RNA Profiling of pooled CRISPR screens to reveal drivers of tumor heterogeneity
Video
Scalable single-cell RNA Profiling of pooled CRISPR screens to reveal drivers of tumor heterogeneity​
PhD student Paulien Van Minsel from KU Leuven, Belgium, discusses the use of single-cell CRISPR screening.
Video
Breakthrough Single Gene Expression for Every Lab ​
Video

Breakthrough Single Gene Expression for Every Lab ​

Robert Meltzer, Associate Principal Scientist, and Shane Liddelow, Associate Professor, present on the new Illumina Single-cell Prep chemistry.