Targeted NGS library preparation, gene expression and genotyping

Achieve an Economy of Scale

Increase productivity and efficiency with automated, cost-effective and easy-to-use workflows for next-generation sequencing (NGS) library preparation, gene expression analysis and genotyping by allele-specific PCR.

Using Juno™ you can produce dozens to hundreds of sample libraries daily for hypothesis-free RNA-seq or targeted DNA NGS. 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.


Reduce costs with nanoliter-scale reaction volumes and walkaway automation.


Perform NGS library preparation or pair with a Biomark HD to implement genotyping, sample identification, gene expression and copy number variant analysis and digital PCR.


Deliver reproducible results day after day using robust microfluidic automation that you can rely on.


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 gene expression, genotyping and digital PCR applications using the Fluidigm Biomark HD.


  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 to amplify DNA targets and barcode sample libraries.


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. 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. 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, reach out to one of our support specialists here


IFCs, Assays and Reagents

Juno Targeted Sequencing IFC

Prepare targeted DNA sequencing libraries with maximum efficiency in batch sizes that match your throughput needs. The LP 48.48 and LP 192.24 IFCs provide multiple formats for targeted DNA sequencing library preparation.

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

SNP Type™ assays provide a high-throughput, low-cost single-nucleotide polymorphism (SNP) genotyping solution enabling rapid assay design for efficient variant screening. The assays are based on allele-specific PCR SNP detection chemistry and are available for use with Fluidigm IFC technology on Biomark HD, EP1™ and Juno™ systems.

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 using the SNP Trace Panel.

Targeted DNA Sequencing Library Kit

Affordably scale your targeted NGS sequencing library preparation using Illumina sequencers.
  1. Juno Targeted Sequencing IFC
  2. Juno Genotyping IFC
  3. Dynamic Array IFCs
  4. SNP Type Assays
  5. SNP Trace™ Panel
  6. Targeted DNA Sequencing Library Kit

Related Systems


Juno Increase productivity and efficiency with automated cost-effective and easy-to-use workflows for DNA and RNA next-generation sequencing (NGS) library preparation.

Biomark HD

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


Polaris Seamlessly integrate cell biology and molecular analysis at the single-cell level. Within one workflow Polaris™ processes single cells for mRNA sequencing applications.


EP1 The EP1™ endpoint system provides efficient and economical endpoint PCR detection downstream of the Juno™ system.
  1. Juno
  2. Biomark HD
  3. Polaris
  4. EP1


Advanta RNA-Seq Library Normalization Workbook V C3

This custom Microsoft® Excel® workbook is designed for use with the Advanta™ RNA-Seq NGS Library Prep Kit and Advanta RNA-Seq XT NGS Library Prep Kits with the Juno™ system to automate calculations and tracking of volume adjustment requirements of sample libraries prior to pooling.

Juno Software

Juno Software v3.14.1, updated September 6, 2019 

Download the most up-to-date software version 3.14.1 to enable running hypothesis-free RNA-seq and targeted DNA NGS library prep applications.

  1. Advanta RNA-Seq Library Normalization Workbook V C3
  2. Juno Software



Thermal control Peltier-based, ranging from 4 °C to 99 °C
Maximum heating rate: >4 °C/sec
Maximum cooling rate: >3 °C/sec
Depth 69.8 cm (27.5 in)
Width 43.9 cm (17.3 in)
Height 50 cm (19.7 in)
Weight 52 kg (115 lb)
Voltage 100–240 V AC
Frequency 50–60 Hz
Maximum current 8.0 A
Typical average power consumption Idle: 40 W
Operating: 175 W

Data Storage

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


System Juno™ software v3.9.1 or later

Work Environment (indoor use only)

Minimum rear clearance 10 cm (4 in)
Minimum front clearance 25 cm (10 in)
Ambient temperature 15–28 ºC (59–82 ºF)
Humidity 20–80%, noncondensing
Pollution degree 2
Electrical installation Category II
Altitude Up to 2,000 m (6,562 ft)

IFC Compatibility


Juno 96.96 GT IFC 

96.96 GT IFC
48.48 GT IFC
192.24 GT IFC
Flex Six™ GT IFC 

Gene Expression

96.96 GE IFC
48.48 GE IFC
192.24 GE IFC
24.192 GE IFC
Flex Six GE IFC

Digital PCR

12.765 dPCR IFC
48.770 dPCR IFC
qdPCR 37K™ IFC

Targeted Sequencing

LP 48.48 IFC
LP 192.24 IFC