Targeted NGS Library Preparation, Gene Expression and Genotyping


Achieve economy of scale

Juno™ delivers affordable scalability for targeted DNA next-generation sequencing (NGS) library preparation, gene expression analysis and genotyping by allele-specific PCR.

Using the Juno Targeted NGS Library Preparation System, you can produce hundreds of targeted DNA sequencing sample libraries daily, with each sample enriched for up to 2,400 specific amplicons covering user-defined genomic loci. Optimized for use with Illumina® sequencing systems in combination with Fluidigm-supplied sample barcodes, Juno enables accurate sequencing of more samples—faster and more affordably than ever before.

Juno also serves as a universal controller to prepare integrated fluidic circuits (IFCs) for both gene expression and genotyping analysis when used together with the Fluidigm Biomark™ HD system. While providing significant advantages in sample throughput for the analysis of dozens to hundreds of DNA variants or RNA transcripts per sample, the Juno system also significantly reduces reaction volumes and required hands-on time, resulting in substantial savings over traditional methods.


Expand sample throughput on the Juno automated microfluidics system.


Boost affordability by reducing reagent and sample volumes and labor requirements, for lower overall cost.


Easily design assay panels for targeted NGS, SNP genotyping or gene expression to detect DNA variants, mRNAs or miRNAs—from a few targets to several thousand.



Juno integrates IFC control and thermal cycling to enable scalable, automated NGS library preparation for Illumina sequencers and IFC preparation for both gene expression and genotyping analysis using the Fluidigm Biomark HD.


  1. Transfer
  2. Run
  3. Read


SNP Genotyping Workflow
Dispense the purified DNA, sample barcodes, SNP Type™ or probe based assays and master mix into designated inlets on the IFC before placing it onto the Juno loading tray.


SNP Genotyping Workflow
Press Start. Juno automatically mixes nanoscale PCR reactions within the IFC and performs amplification using the integrated thermocycler. For compatibility with low sample inputs down to 5.5 ng, the option for a low-cycle-number preamplification exists. This option is fully integrated and automated on the IFC.


SNP Genotyping Workflow
Transfer the IFC with completed SNP reactions to the Biomark HD or EP1™ for endpoint genotyping analysis.

  1. Transfer
  2. Run
  3. Sequence


NGS Library Preparation Workflow
Dispense the purified DNA, sample barcodes, PCR primers and master mix into designated inlets on the IFC before placing it onto the Juno loading tray.


NGS Library Preparation Workflow
Press Start. Juno automatically mixes nanoscale reactions within the IFC and amplifies up to 2,400 amplicons for up to 192 samples using the 192.24 library preparation IFC and the integrated thermal cycler.


NGS Library Preparation Workflow
Targeted DNA sequencing libraries are collected from the IFC and adapter PCR and cleanup are performed in a single tube reaction, followed by sequencing on an Illumina system.

  1. Transfer
  2. Load
  3. Run | Read


Gene Expression Workflow
Dispense purified cDNA from RNA or miRNAs, qPCR assays and master mix into designated inlets on the IFC before placing it onto the Juno loading tray.


Gene Expression Workflow
Press Start. Juno automatically loads the IFC with input sample, assays and reagents to prepare for thousands of nanoscale real-time PCR reactions.

Run | Read

Gene Expression Workflow
Transfer the IFC with pre-mixed real-time PCR reactions to the Biomark HD for amplification and real-time quantitative detection.


Juno Support

Click the link below to view training tutorials, browse FAQs, read technical documents, review service plans and locate the right IFCs, kits and reagents for your research. If you still need help, contact a Support Specialist.


IFCs, Assays and Reagents

Juno Targeted Sequencing IFC

Prepare up to 192 targeted DNA sequencing libraries with integrated sample barcoding using a single Library Prep—192.24 IFC. Target as many as 2,400 amplicons per purified DNA sample.

Juno Genotyping IFC

Analyze up to 96 DNA samples (9,216 datapoints) simultaneously across 96 different SNP Type or probe-based assays with the Juno 96.96 Genotyping IFC.

Dynamic Array IFCs

Experience a new level of efficiency and throughput for gene expression and genotyping applications with the Fluidigm Dynamic Array™ IFCs used together with the Juno and Biomark HD systems.

SNP Type Assays

Leverage a flexible, economical solution for single nucleotide polymorphism (SNP) genotyping with Fluidigm's SNP Type™ assays.

Targeted DNA Sequencing Library Kit

Affordably scale your targeted NGS sequencing library preparation using Illumina sequencers.

SNP Trace™ Panel

Ensure accurate sample identification with an authoritative panel of 96 SNPs that determine specific attributes around gender, ancestry or polymorphism across populations.

  1. Juno Targeted Sequencing IFC
  2. Juno Genotyping IFC
  3. Dynamic Array IFCs
  4. SNP Type Assays
  5. Targeted DNA Sequencing Library Kit
  6. SNP Trace™ Panel

Related Systems


EP1 The EP1™ endpoint system provides efficient and economical endpoint PCR detection downstream of the Juno™ system.

Biomark HD

Biomark HD Analyze gene expression with real-time PCR, industry-leading flexibility and consistently high-quality results on the Biomark™ HD system.
  1. EP1
  2. Biomark HD


SNP Genotyping Analysis

Our innovative SNP Type software is designed specifically for analyzing genotyping data acquired from Biomark or EP1 systems. Advanced features include cluster-calling algorithm technology, multiple IFC scoring and automatic confidence score ratings.

  1. SNP Genotyping Analysis



Height 50 cm (19.7in)
Width 43.9 cm (17.3 in)
Depth 69.8 cm (27.5 in)
Weight 62 kg (137 lb)

Thermal Control

Peltier-based 4–99 ºC
Max heating rate >4 ºC/sec
Max cooling rate >3 ºC/sec

IFC Compatibility

Library Prep IFCs 192.24
Dynamic Array™ IFCs 48.48, 96.96, 192.24, Flex Six™
Digital Array™ IFCs 12.765, 48.770, qdPCR 37K™

Data Storage

Ethernet connection 1 GB/sec
Hard drive 40 GB
Port USB port
Computer Internal CPU with touchscreen interface