Sensitivity meets Speed
Rapidly prepare stranded, whole transcriptome sequencing libraries using Watchmaker RNA Library Prep Kits with Polaris® Depletion. The highly streamlined Polaris Depletion module depletes highly abundant rRNA and globin transcripts in human, mouse, and rat samples, providing improved coverage of biologically interesting transcripts, including long non-coding RNAs.
The automation-friendly workflow reduces total turnaround time, hands-on time, and consumable use through a reduction in bead purification and reaction steps. A novel, engineered reverse transcriptase improves the conversion of RNA to cDNA, enabling high-quality performance with 1 ng to 1 µg of total RNA, as well as FFPE-derived RNA.
Key Features and Benefits
- Increase sensitivity with clinically relevant samples, including FFPE and inputs as low as 1 ng
- Generate high-complexity libraries in under 4.5 hours, including rRNA and globin depletion
- Improve automatability with fewer purifications and reagent additions
- Consolidate disparate/niche workflows into one process with broad sample type and input compatibility
- Realize the performance benefits of a reverse transcriptase specifically tailored for RNA-seq applications
As presented on September 17, 2024
Applications
- RNA sequencing with degraded samples, such as FFPE
- Detection of long non-coding RNAs (lncRNAs)
- Gene fusion, splice variant, and isoform detection
- Gene expression analysis
- Novel transcript discovery
- Single nucleotide variant (SNV) detection
- Targeted sequencing protocols employing hybridization capture
Process more samples easily with a simple, rapid workflow
Figure 1. Improve automatability and reduce turnaround time. The Watchmaker solution combines and shortens enzymatic steps and has fewer bead purifications in comparison to other commercially available kits, resulting in a highly automatable workflow with significantly reduced hands-on time (up to one hour per plate) and consumable use (up to 1,000 pipette tips per plate).
Key Performance Data
Access more information from FFPE samples
Processing FFPE samples is inherently challenging due to the template damage incurred during fixation and the presence of residual cross-links. Watchmaker’s novel FFPE treatment step, paired with a reverse transcriptase specifically engineered for RNA-seq applications, delivers excellent sensitivity and enables researchers to address a broader range of clinically relevant samples effectively.
Access more information from FFPE samples
Increase sensitivity with ultra-low-input samples
Robust and reproducible sample processing can be difficult for applications and samples where RNA quantities are restrictive, such as fine needle biopsies, limiting the sensitivity of associated assays. Watchmaker RNA Library Prep Kits with Polaris® Depletion enable the generation of high quality libraries with as little as 1 ng of RNA.
Increase sensitivity with ultra-low-input samples
Retain quantitative gene expression information across input amounts
Agreement between high- and low-input libraries with respect to unique genes identified and their abundance is indicative of how well sample complexity is maintained as RNA input amounts decrease. Ideally, the relative gene expression profile should remain consistent across input amounts for a given sample. Watchmaker better preserves the gene expression profile as RNA input amount decreases from 500 ng to 10 ng, whereas other commercial solutions result in data distortion with low inputs.
Figure 4. Prevent data distortion with ... MORE
Retain quantitative gene expression information across input amounts
Figure 4. Prevent data distortion with low inputs. Libraries were prepared from a whole blood sample in triplicate using 500 ng and 10 ng of RNA. Data were randomly downsampled to 16M paired reads per library. Differential expression analysis between averaged 500 ng (control) and 10 ng whole blood samples using DESeq2. Results indicate that other vendors lose representation of low abundance genes at 10 ng, while the Watchmaker solution does not.
Efficiently sequence blood samples while covering lncRNAs
Overabundant globin mRNAs in blood samples pose a challenge for efficient RNA sequencing, as ≥ 30% of bases map to these transcripts if traditional mRNA capture is used. Additionally, mRNA capture omits a significant subset of long non-coding RNAs (lncRNAs) that have demonstrated regulatory functions.¹ Polaris Depletion removes both rRNA and globin mRNA while also providing excellent coverage of lncRNAs, such as MALAT1 which has been implicated in at least 17 cancer types, including lung, breast, and pancreatic.²
- Statello, L., Guo, CJ., Chen, LL. et al. Gene regulation by long non-coding RNAs and its biological functions. Nat Rev Mol Cell Biol 22, 96–118 (2021).
- Amodio, N., Raimondi, L., Juli, G. et al. MALAT1: a druggable long non-coding RNA for targeted anti-cancer approaches. J Hematol Oncol 11, 63 (2018).
Efficiently sequence blood samples while covering lncRNAs
BROCHURES
Watchmaker RNA Library Prep Kit with Polaris Depletion Brochure
Fusion Detection Gene Expression Analysis Long Noncoding RNA Analysis Element Illumina Singular Ultima RNA Blood FFPE RNA NGS RNA Library Prep RNA Library Prep with Polaris DepletionThe Watchmaker RNA Library Prep Kit with Polaris® Depletion enables rapid preparation of high-quality whole transcriptome libraries by depleting rRNA and globin transcripts. Its streamlined workflow supports low-input RNA and FFPE samples, enhancing coverage and reducing turnaround time.
TECHNICAL LITERATURE
Maximizing RNA sequencing economy from blood samples using a combined mRNA capture and globin depletion workflow
Gene Expression Analysis Illumina RNA Blood mRNA Library Prep RNA Library Prep with Polaris DepletionThis technical note presents an optimized workflow that combines mRNA capture with globin and rRNA depletion to maximize sequencing efficiency from blood-derived RNA. By reducing non-coding and globin transcript content, this approach improves mRNA enrichment, decreases duplication rates, and enhances gene detection and transcript coverage uniformity across varied RNA inputs.
VIDEOS
Interrogating tumor structural variation and nongenic dark matter with whole-transcriptome profiling
Fusion Detection Long Noncoding RNA Analysis Whole Transcriptome/Total RNA Sequencing Illumina RNA FFPE RNA NGS RNA Library Prep with Polaris DepletionThis video provides insights on whole transcriptome sequencing with FFPE samples for fusion detection applications, as well as covers RNA sequencing on noncoding transcripts.
Fusion detection in pediatric oncology: Insights from transcriptome sequencing
Fusion Detection Novel Transcript Discovery Whole Transcriptome/Total RNA Sequencing Illumina FFPE RNA NGS RNA Library Prep with Polaris DepletionAs presented at AMP 2024, hear Katie Miller, PhD from Nationwide Children’s Hospital present on the value of whole transcriptome sequencing (WTS) for fusion detection, including: the benefits of WTS over DNA sequencing and targeted RNA sequencing; the importance of a workflow that can handle low inputs and damaged FFPE samples while providing robust inter-user performance; and the potential utility of gene expression information in addition to fusion calling.
Sequenomics: Maximizing data quality, minimizing process complexity in NGS
Illumina DNA RNA Blood FFPE Plasma/cfDNA DNA NGS RNA NGS DNA Library Prep DNA Library Prep with Fragmentation mRNA Library Prep RNA Library Prep with Polaris DepletionThis video highlights Watchmaker’s approach to “sequenomics” — the integration of biochemistry, workflow design, and automation to enhance sequencing efficiency while reducing complexity and hands-on time.
AUTOMATION RESOURCES
Automating Watchmaker’s RNA Library Prep Kit with Polaris Depletion on the Biomek i7 Hybrid NGS Workstation
Lab Automation RNA Cell Line RNA NGS RNA Library Prep with Polaris Depletion BeckmanThis application note details the automation of the Watchmaker RNA Library Prep Kit with Polaris® Depletion on the Biomek i7 Hybrid NGS Workstation, enabling preparation of up to 96 libraries in under 7 hours. The workflow reduces hands-on time, minimizes errors, and offers flexibility in sample processing for high-throughput RNA sequencing.
Evaluating a simple, automatable, and sensitive solution for rapid RNA-seq
Illumina RNA RNA NGS RNA Library Prep with Polaris Depletion RevvityThis poster showcases the automation of the Watchmaker RNA Library Prep Kit with Polaris® Depletion on the Revvity Sciclone G3 NGSx, enabling high-quality whole transcriptome libraries from a wide range of RNA inputs. The workflow demonstrated consistent yields, no cross-contamination, and scalability up to 96 samples in under 7 hours, making it ideal for clinical and research applications. As presented at SLAS 2025.
Evaluating a rapid automated RNA-seq workflow for ultra-low input sample types
Gene Expression Analysis Lab Automation Illumina RNA RNA NGS RNA Library Prep with Polaris Depletion HamiltonThis poster demonstrates the successful automation of the Watchmaker RNA Library Prep Kit with Polaris® Depletion on the Hamilton Microlab® NGS STAR MOA for ultra-low input RNA samples. It shows that the automated workflow delivers high-quality, reproducible libraries comparable to manual prep, with reduced hands-on time and consistent performance across key sequencing metrics. As presented at SLAS 2025.
Automated RNA library preparation for whole transcriptome sequencing using Watchmaker Genomics’ RNA Library Prep Kit with Polaris Depletion on the epMotion 5075t workstation
Lab Automation Illumina RNA RNA NGS RNA Library Prep with Polaris Depletion EppendorfThis application note details the development of a streamlined, automated workflow for RNA library preparation using the Watchmaker RNA Library Prep Kit with Polaris® Depletion on the Eppendorf epMotion® 5075t. The protocol demonstrates robust performance across low-input and degraded samples, enabling high-throughput, high-quality whole transcriptome sequencing with minimal hands-on time.
POSTERS
Surveying the RNA-seq landscape: A multi-workflow comparison for mRNA and whole transcriptome sequencing applications
Gene Expression Analysis mRNA Sequencing Whole Transcriptome/Total RNA Sequencing Element Illumina Singular RNA Blood Cell Line FFPE Frozen Tissue RNA NGS mRNA Library Prep RNA Library Prep RNA Library Prep with Polaris DepletionThis poster presents a comparative analysis of commercially available stranded RNA library preparation kits for mRNA and whole transcriptome sequencing, focusing on their performance with low-input and degraded samples, such as FFPE. Additionally, it explores compatibility with both Element and Singular short-read sequencing platforms.
Increasing complexity and quality of total RNA sequencing at scale (Broad Clinical Labs)
Gene Expression Analysis Lab Automation mRNA Sequencing Whole Transcriptome/Total RNA Sequencing Illumina RNA Blood RNA NGS RNA Library Prep with Polaris Depletion AgilentThis poster from Broad Clinical Labs presents a comparison between the Watchmaker RNA Library Prep with Polaris® Depletion and a standard poly(A) mRNA capture with globin depletion method using whole blood samples. The study demonstrates that the Watchmaker workflow yields more complex libraries, identifying 15% more transcripts and 3% more protein-coding genes than the standard method. Additionally, the automated Watchmaker workflow significantly reduces hands-on processing time, with a single lab user capable of generating approximately 960 libraries per week using two machines.
Cost-effective, high-resolution whole transcriptome sequencing for gene fusion detection applications (Ultima Genomics)
Fusion Detection Gene Expression Analysis Variant Calling Whole Transcriptome/Total RNA Sequencing Ultima RNA RNA NGS RNA Library Prep with Polaris DepletionThis poster presents the optimization of the Watchmaker RNA Library Prep Kit with Polaris® Depletion for use with Ultima Genomics' high-capacity sequencing platform, enabling cost-effective whole transcriptome sequencing (WTS) for gene fusion detection.
Optimized RNA-seq library preparation for fusion calling from FFPE samples
Fusion Detection Gene Expression Analysis Targeted Sequencing Whole Transcriptome/Total RNA Sequencing Illumina RNA FFPE RNA NGS RNA Library Prep with Polaris DepletionThis poster explores the use of whole transcriptome analysis (WTA) for detecting gene fusions in formalin-fixed, paraffin-embedded (FFPE) samples, comparing it to targeted enrichment methods. The study demonstrates that WTA can identify known fusions and, with optimized library preparation for longer insert sizes, facilitate de novo fusion detection. Additionally, the research shows that WTA enables gene expression analysis and fusion identification from a single dataset, offering a comprehensive approach to transcriptomic profiling in challenging FFPE samples.
Improved detection of unique transcripts using a novel, rapid whole transcriptome sequencing workflow
Gene Expression Analysis Whole Transcriptome/Total RNA Sequencing Illumina RNA Blood FFPE RNA NGS RNA Library Prep with Polaris DepletionThis poster presents the Watchmaker RNA Library Prep Kit with Polaris® Depletion, offering a streamlined, automatable workflow for whole transcriptome sequencing from challenging samples like FFPE. It enhances gene detection sensitivity, reduces hands-on time, and supports low-input RNA, enabling library construction in under five hours.
A comparative analysis of library preparation technologies for RNA sequencing from FFPE samples
Gene Expression Analysis Whole Genome Sequencing Illumina RNA FFPE Frozen Tissue RNA NGS RNA Library Prep with Polaris DepletionThis poster compares RNA sequencing solutions for FFPE samples, highlighting that the Watchmaker RNA Library Prep Kit with Polaris® Depletion provides superior gene detection and reproducibility, with minimal data distortion.
Broadening the NGS Landscape with Watchmaker Library Prep and the Element AVITI System
Gene Expression Analysis SNV/SNP/InDel Detection Variant Calling Whole Genome Sequencing Whole Transcriptome/Total RNA Sequencing Element DNA RNA Cell Line DNA NGS RNA NGS DNA Library Prep with Fragmentation RNA Library Prep with Polaris DepletionThis poster presents the integration of Watchmaker Genomics' DNA and RNA library preparation kits with the Element AVITI™ System, enhancing sequencing efficiency with tunable insert sizes, uniform GC coverage, and high data quality. The workflows support a wide range of applications, including whole genome and transcriptome sequencing.
Improving data quality and reproducibility with FFPE-derived RNA using a novel, rapid whole transcriptome library prep workflow
Gene Expression Analysis Whole Transcriptome/Total RNA Sequencing Illumina RNA Blood FFPE RNA NGS RNA Library Prep with Polaris DepletionThis poster introduces a rapid RNA library preparation workflow tailored for FFPE-derived RNA and compares it to three other commercial products using RNA from whole blood and FFPE blocks. The study demonstrated that the Watchmaker solution increased gene detection sensitivity with FFPE-derived RNA, accurately profiled gene expression across a wide range of input amounts, and enabled library construction in under 5 hours, reducing hands-on time and consumable use by 25%.
Investigation of critical RNA sequencing variables and their impact on fusion calling
Fusion Detection Gene Expression Analysis mRNA Sequencing Targeted Sequencing Whole Transcriptome/Total RNA Sequencing Illumina RNA FFPE RNA NGS RNA Library Prep with Polaris DepletionThis poster evaluates RNA sequencing workflow variables and their impact on gene fusion detection using both whole transcriptome and target enrichment approaches. It demonstrates that library prep choices, input mass, and cleanup strategies significantly influence fusion call efficiency, with mRNA capture and rRNA depletion improving outcomes for high-quality and FFPE samples.
Generating higher quality transcriptomic data from challenging sample types
Gene Expression Analysis Lab Automation Whole Transcriptome/Total RNA Sequencing Illumina RNA RNA NGS RNA Library Prep with Polaris DepletionThis poster highlights the performance of Watchmaker’s total RNA workflows across a wide range of RNA qualities, including low RIN and salt-contaminated samples. It demonstrates improved consistency, higher library yields, and better transcript coverage compared to standard poly(A) methods, enabling high-quality transcriptomic data from challenging sample types.
PROTOCOLS
Watchmaker RNA Library Prep Kit with Polaris Depletion User Guide
DNA RNA NGS RNA Library Prep with Polaris Depletion Agilent Eppendorf Hamilton RevvityProtocol for Watchmaker RNA Library Prep Kit with Polaris® Depletion, which enables highly streamlined preparation of stranded, whole transcriptome sequencing (WTS) libraries from 1 ng to 1 µg of total RNA with high library complexity and low coverage bias, from both high- and low- quality samples, including FFPE material.
| RNA input range | 1 ng - 1 µg |
|---|---|
| Polaris® Depletion Kit - rRNA/Globin (HMR) contents | Depletion Master Mix Depletion Probes - rRNA/Globin (HMR) Probe Digestion Master Mix |
| Watchmaker RNA Library Prep Kit contents | FFPE Treatment Buffer Frag & Prime Buffer 1st Strand Buffer 1st Strand Enzyme 2nd Strand Enzyme 2nd Strand Buffer Ligation Enzyme Ligation Buffer Equinox® Library Amplification Master Mix (2X) P5/P7 Primer Mix (10X) |
| Shipping conditions | Ice packs |
| Storage | -20°C ± 5°C |
| Shelf life | (24 rxn): ≥ 6 months (> 24 rxn): ≥ 12 months |
Can the Watchmaker RNA Library Prep Kit with Polaris® Depletion be used to detect coding RNAs?
This kit depletes total RNA of ribosomal and globin RNA. Both coding RNA and long non-coding RNA are represented in the sequencing data.
To focus on only coding RNA, please use the Watchmaker mRNA Library Prep Kit for coding RNA.
What other RNA Library Prep Kits does Watchmaker offer?
The Watchmaker mRNA Library Prep Kit includes poly(A) enrichment to focus sequencing on coding RNA. This kit is compatible with intact RNA samples.
The Watchmaker RNA Library Prep Kit is suitable for total RNA and typically used upstream of target enrichment. This kit is compatible with both high quality and degraded RNA samples.
Can this kit be automated?
The Watchmaker RNA Library Prep Kit with Polaris Depletion is highly automatable. The kit was developed with automation in mind and 96 reaction kits include generous overages to account for dead volumes on liquid handling platforms. Visit our automation page for a list of scripts already developed or to contact a member of our automation team regarding your platform and needs.
Is this kit compatible with other (non-Illumina) sequencing platforms?
This kit has been demonstrated to be compatible with Element, Singular and Ultima sequencing platforms.
Does this product support long-read sequencing?
We use random primers to prime during first strand synthesis, which does not support full-length cDNA generation. This makes it unlikely to be compatible with-long read applications.
Do you offer custom formats?
Yes! Watchmaker offers customer fills, packaging, concentrations, and labeling – including private label – designed to meet your unique needs. We offer flexible terms to serve organizations of any size, and our right-sized processes enable rapid turnaround time on customization. Please contact sales@watchmakergenomics.com to learn more about our capabilities.
Are you ISO 13485-certified?
Yes! Our Quality Management System has achieved ISO 13485:2016 Certification. Our certificate has been awarded for the design, development, manufacture, contract manufacture, and support of high performing reagents for genomics applications in medical research. Download the certificate here.
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| Description | 24 rxn | 96 rxn | 384 rxn | |
|---|---|---|---|---|
| Watchmaker RNA Library Prep Kit with Polaris® Depletion incl. reagents for rRNA and globin depletion, RNA library prep, and amplification | 7BK0002-024 | 7BK0002-096 | 7BK0002-384 | Request a quote |
Please contact sales@watchmakergenomics.com to inquire about custom kit configurations.
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