BROCHURES
Watchmaker RNA Library Prep Kit with Polaris Depletion Brochure
Fusions Gene Expression LncRNA Element Illumina Singular Ultima RNA Blood FFPE RNA NGS RNA LPK Polaris LPKThe 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.
Equinox Library Amplification Kits Brochure
Element Illumina Singular Ultima DNA RNA FFPE Microbial DNA NGS Equinox Equinox UEquinox® Library Amplification Kits offer ultra-high-fidelity DNA polymerase in a hot start PCR master mix, ensuring high-efficiency, low-bias NGS library amplification across diverse inputs and GC content.
OEM and Custom Solutions Brochure
Custom DNA RNA Blood Dried Blood Spot FFPE Microbial Plasma/cfDNA Plasmid Saliva/buccal DNA NGS Enzymes MDx RNA NGSWatchmaker Genomics delivers high-performance, customizable genomics solutions, including library prep kits and enzymes, with ISO 13485 quality system compliance.
mRNA Library Prep Kit Brochure
Fusions Gene Expression Isoforms LncRNA mRNA Novel Transcrips SNP/InDel Element Illumina Singular Ultima RNA Blood Dried Blood Spot RNA NGS mRNA LPK RNA LPKThe Watchmaker mRNA Library Prep Kit creates stranded mRNA-seq libraries in under 5 hours with 2.5 ng–1 µg RNA, offering automation-ready, streamlined workflows and high sensitivity.
phi29 DNA Polymerase Brochure
Isothermal Amp RCA Single Cell Enzymes phi29 DNAPWatchmaker Genomics' phi29 DNA Polymerase exhibits strong strand displacement activity and high processivity, enabling efficient isothermal DNA amplification from low template amounts. Its 3′→5′ exonuclease activity ensures high-fidelity amplification, making it suitable for sequencing DNA template preparation.
Precision Enzymes and Proteins Brochure
Custom Enzymes MDx DNAP I Equinox Equinox U phi29 DNAP RNase Inhibitor StellarScript StellarScript HT StellarScript HT+ StellarTaq T4 DNA Ligase T4 DNAP T4 PNK T4 gp32 Taq DNAPWatchmaker Genomics offers a portfolio of precision-engineered enzymes and proteins, designed to meet the demands of high-stringency applications. We provide tailored services such as custom fills, formats, packaging, and labeling to accommodate unique specifications.
RNase Inhibitor Brochure
Pathogen Detection RT-PCR/RT-qPCR Single Cell RNA Blood FFPE Microbial Saliva/buccal Enzymes MDx RNA NGS RNase InhibitorWatchmaker Genomics' RNase Inhibitor binds RNases A, B, and C, protecting RNA integrity in applications like RT-qPCR and single-cell sequencing at temperatures up to 55°C. Its murine origin enhances performance in low-DTT conditions, and custom formats support lyophilization.
StellarScript HT+ Reverse Transcriptase Brochure
Pathogen Detection RT-PCR/RT-qPCR RNA Blood FFPE Microbial Saliva/buccal Enzymes MDx StellarScript HT+StellarScript® HT+ Reverse Transcriptase is an engineered M-MLV variant with reduced RNase H activity, offering enhanced processivity, thermostability, and inhibitor tolerance, enabling efficient cDNA synthesis from low-input or degraded RNA samples.
StellarScript® Reverse Transcriptase Portfolio Brochure
RT-PCR/RT-qPCR RNA Blood FFPE Microbial Saliva/buccal Enzymes MDx StellarScript StellarScript HT StellarScript HT+StellarScript® Reverse Transcriptase is an engineered M-MLV variant with reduced RNase H activity, offering enhanced processivity, thermostability, and inhibitor tolerance for applications such as first-strand cDNA synthesis, RT-qPCR, and RNA sequencing.
T4 DNA Ligase Brochure
Enzymes T4 DNA LigaseWatchmaker Genomics' T4 DNA Ligase catalyzes the formation of phosphodiester bonds between nucleic acids, efficiently joining blunt or cohesive ends and repairing single-stranded nicks in duplex DNA, RNA, or DNA/RNA hybrids. Available in concentrations of 120 and 600 U/µL, it is suitable for applications such as cloning, adapter ligation, site-directed mutagenesis, and nick repair.
Watchmaker DNA Library Prep Kit with Fragmentation Brochure
PCR-free WGS WES WGS Element Illumina Singular Ultima DNA Blood FFPE Microbial DNA NGS Frag LPKThe Watchmaker DNA Library Prep Kit offers efficient, high-quality library preparation with tunable DNA shearing and low sequence artifacts. It supports PCR-free libraries in under 90 minutes, ideal for low-input and FFPE samples.
Watchmaker DNA Library Prep Kit Brochure
Liquid Biopsy Methyl PCR-free WGS WES WGS Element Illumina Singular Ultima DNA Blood FFPE Microbial DNA NGS DNA LPKThe Watchmaker DNA Library Prep Kit enhances sequencing sensitivity, especially for low-input cfDNA from liquid biopsies, by efficiently converting DNA into sequenceable library molecules. It supports applications like cfDNA analysis, DNA methylation studies, ChIP-seq, and low-frequency variant detection, with a streamlined workflow that prepares libraries in under two hours.
StellarTaq DNA Polymerase Brochure
Pathogen Detection PCR/qPCR RT-PCR/RT-qPCR DNA Blood Saliva/buccal Urine Enzymes MDx StellarTaqThis brochure highlights the capabilities of StellarTaq DNA polymerase with respect to polymerization speed and inhibitor tolerance making it an excellent option for pathogen detection platforms and assays.
TECHNICAL LITERATURE
Enzymatic fragmentation enables scalable preparation of high-quality FFPE libraries with minimal artifacts
Targeted Illumina DNA Cell Line FFPE DNA NGS Frag LPKThis application note highlights the use of the Watchmaker DNA Library Prep Kit with Fragmentation for FFPE samples, offering enzymatic fragmentation that reduces artifacts and enhances sequencing data quality. The streamlined protocol minimizes sample loss and improves efficiency compared to traditional sonication methods.
Maximizing RNA sequencing economy from blood samples using a combined mRNA capture and globin depletion workflow
Gene Expression Illumina RNA Blood mRNA LPK Polaris LPKThis 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.
Non-invasive prenatal testing: Embracing low-input methodologies
NIPT Illumina DNA Plasma/cfDNA DNA NGS DNA LPKThis case study highlights how Trisomy Test Ltd improved its NIPT workflow using the Watchmaker DNA Library Prep Kit to generate reliable results from cfDNA inputs as low as 0.5 ng. The streamlined workflow enabled faster turnaround, higher success rates in low fetal fraction samples, and efficient processing of nearly 7,000 clinical specimens.
VIDEOS
Interrogating tumor structural variation and nongenic dark matter with whole-transcriptome profiling
Fusions LncRNA WTS Illumina RNA FFPE RNA NGS Polaris LPKThis video provides insights on whole transcriptome sequencing with FFPE samples for fusion detection applications, as well as covers RNA sequencing on noncoding transcripts.
Customizing Watchmaker DNA PCR-free Library Prep Kit for improved NovaSeq X performance
PCR-free WGS WGS Illumina DNA DNA NGS Frag LPKAs presented at ESHG 2024, this video provides recommendations and commentary on whole genome sequencing on the NovaSeq X platform.
Overcoming sequencing artifacts to fuel clinically relevant NGS applications
Illumina DNA DNA NGS Frag LPK EquinoxThis video covers the data quality and workflow improvements made as a result of implementing the Watchmaker DNA Library Prep Kit with Fragmentation - including reduced sequence artifacts and PCR errors, as well as increased scalability.
Non-invasive pre-natal testing: Embracing low-input methodologies
NIPT WGS Illumina DNA Blood Plasma/cfDNA DNA NGS DNA LPKAs presented at ESHG 2024, this video provides a case study on the use of the Watchmaker DNA Library Prep Kits for non-invasive prenatal testing to improve turnaround times and reduce the percentage of uninformative results.
Fusion detection in pediatric oncology: Insights from transcriptome sequencing
Fusions Novel Transcrips WTS Illumina FFPE RNA NGS Polaris LPKAs 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 LPK Frag LPK mRNA LPK Polaris LPKThis 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
Automation RNA Cell Line RNA NGS Polaris LPK 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.
Automating Watchmaker’s high-performance next generation sequencing chemistries on the Biomek i7 liquid handler for rapid, high-throughput sample to sequence output
Metagenomics WGS Illumina DNA Cell Line Microbial Plasma/cfDNA DNA NGS Frag LPK BeckmanThis poster presents the integration of Watchmaker Genomics' DNA Library Prep Kit with Fragmentation into the Biomek i7 Hybrid NGS Workstation, facilitating rapid, high-throughput library preparation. The automated workflow achieves consistent, high-quality libraries with uniform insert sizes and GC coverage across various sample types and inputs, reducing human error and hands-on time.
Automated Watchmaker mRNA Library Prep Kit on Sciclone® G3 NGSx
Automation RNA Cell Line RNA NGS mRNA LPK RevvityThis application note details the automation of the Watchmaker mRNA Library Prep Kit on the Sciclone® G3 NGSx workstation, enabling the preparation of up to 96 libraries in approximately 5 to 6 hours. The automated workflow reduces hands-on time and minimizes errors, accommodating various sample types and input amounts. The system offers flexibility in bead cleanup ratios and adapter options, enhancing reproducibility and efficiency in mRNA sequencing applications.
Modernizing DNA library preparation: An automated workflow for translational research and clinical genomics
Metagenomics WGS Illumina DNA Cell Line Microbial Plasmid DNA NGS Frag LPK RevvityThis poster presents an automated DNA library preparation workflow using the Watchmaker DNA Library Prep Kit with Fragmentation on the PerkinElmer Sciclone® G3 NGSx workstation. The system processes up to 96 samples per run, accommodating various inputs, including human genomic DNA, metagenomic DNA, and plasmids. The workflow reduces human error and hands-on time, with total processing for 96 samples taking approximately 3.5 to 4.5 hours. Consistent fragmentation and high sequencing uniformity across diverse GC content highlight its utility in translational and research applications.
Streamline Watchmaker’s DNA Library Prep Kit for pre-fragmented DNA on the Sciclone G3 NGSx Workstation
Automation DNA Cell Line DNA NGS DNA LPK RevvityThis application note details the automation of the Watchmaker DNA Library Prep Kit on the Sciclone® G3 NGSx workstation, processing up to 96 samples with flexible input and cleanup options. The workflow reduces hands-on time and minimizes errors, enhancing efficiency and reproducibility in NGS applications.
Automated library preparation using Watchmaker DNA Library Prep Kit with Fragmentation on the firefly®
Automation WGS DNA Cell Line DNA NGS Frag LPK SPT LabtechThis application note outlines the automation of the Watchmaker DNA Library Prep Kit with Fragmentation on the firefly® platform, improving efficiency, reproducibility, and reducing human error in NGS workflows. The integration enables streamlined library prep for precious samples, enhancing laboratory resource utilization.
Watchmaker DNA Library Prep Kit with Fragmentation automated on the Revvity Sciclone™ G3 NGSx workstation
Automation DNA Cell Line DNA NGS Frag LPK RevvityThis application note details the automation of the Watchmaker DNA Library Prep Kit with Fragmentation on the Sciclone® G3 NGSx workstation, processing up to 96 samples per run with reduced hands-on time. The workflow supports flexible adapter options and PCR configurations, ensuring reproducible library yields and size distributions.
Watchmaker® DNA Library Prep Kit with Fragmentation automated on the PerkinElmer Sciclone® G3 NGSx Workstation
Automation WGS DNA Cell Line DNA NGS Frag LPK RevvityThis application note highlights the automation of the Watchmaker DNA Library Prep Kit with Fragmentation on the Sciclone® G3 NGSx workstation, processing up to 96 samples with reduced hands-on time and minimal human error. The workflow supports flexible adapter options and PCR configurations, ensuring reproducible yields and size distributions.
Automating Watchmaker DNA Library Prep Kit with Fragmentation on Biomek i7 Hybrid NGS Workstation
Automation Metagenomics Illumina DNA Cell Line Microbial Plasmid DNA NGS Frag LPK BeckmanThis application note highlights the automation of the Watchmaker DNA Library Prep Kit with Fragmentation on the Biomek i7 Hybrid NGS Workstation, enabling high-throughput preparation of sequencing-ready libraries in under 4 hours. It emphasizes consistent library quality, uniform GC coverage, and minimized hands-on time to streamline DNA library preparation workflows.
Evaluating a simple, automatable, and sensitive solution for rapid RNA-seq
Illumina RNA RNA NGS Polaris LPK 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 Automation Illumina RNA RNA NGS Polaris LPK 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
Automation Illumina RNA RNA NGS Polaris LPK 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 mRNA WTS Element Illumina Singular RNA Blood Cell Line FFPE Frozen Tissue RNA NGS mRNA LPK RNA LPK Polaris LPKThis 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 Automation mRNA WTS Illumina RNA Blood RNA NGS Polaris LPK 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)
Fusions Gene Expression Variant Calling WTS Ultima RNA RNA NGS Polaris LPKThis 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
Fusions Gene Expression Targeted WTS Illumina RNA FFPE RNA NGS Polaris LPKThis 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.
Parallelized reverse transcription engineering and rapid whole transcriptome sequencing workflow optimization delivers improved gene detection sensitivity
Illumina RNA Blood Frozen Tissue Enzymes StellarScript StellarScript HT StellarScript HT+This poster details the development of engineered reverse transcriptases (RTs) and an optimized whole transcriptome sequencing workflow to enhance gene detection sensitivity, particularly with low-input and challenging samples like formalin-fixed, paraffin-embedded (FFPE) tissues.
Improved detection of unique transcripts using a novel, rapid whole transcriptome sequencing workflow
Gene Expression WTS Illumina RNA Blood FFPE RNA NGS Polaris LPKThis 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.
Benchmarking enzymatic library preparation workflows in a PCR-free whole genome sequencing context
PCR-free WGS WGS Illumina DNA Cell Line DNA NGS Frag LPKThis poster evaluates eight commercially available library preparation solutions for PCR-free whole genome sequencing (WGS). Results show the Watchmaker DNA Library Prep Kit with Fragmentation achieves high conversion rates with as little as 75 ng of input DNA, delivering superior yields. Sequencing results indicate minimal GC bias and increased coverage across challenging GC-rich regions, highlighting the kit's effectiveness in producing high-quality, uniform, and unbiased WGS data.
A comparative analysis of library preparation technologies for RNA sequencing from FFPE samples
Gene Expression WGS Illumina RNA FFPE Frozen Tissue RNA NGS Polaris LPKThis 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.
An evaluation of enzymatic fragmentation in the library preparation workflow: The Watchmaker Genomics Kit (Broad Institute)
Automation PCR-free WGS SNP/InDel Variant Calling WGS Illumina DNA Cell Line DNA NGS Frag LPK AgilentThis poster from the Broad Institute evaluates the Watchmaker DNA Library Prep Kit with Fragmentation, focusing on its enzymatic fragmentation method as an alternative to traditional mechanical shearing in whole genome sequencing (WGS). The study demonstrates that the enzymatic approach offers comparable sequencing metrics. The workflow is user-friendly, completing high-quality library construction in under two hours, and is suitable for scaling in throughput.
Broadening the NGS Landscape with Watchmaker Library Prep and the Element AVITI System
Gene Expression SNP/InDel Variant Calling WGS WTS Element DNA RNA Cell Line DNA NGS RNA NGS Frag LPK Polaris LPKThis 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.
Correlation of pathogenic somatic mutation presence in tumor tissue and plasma-derived extracellular vesicles (FYR Diagnostics)
Liquid Biopsy Variant Calling WGS Element DNA FFPE Plasma/cfDNA DNA NGS DNA LPKThis poster from FYR Diagnostics explores the potential of using DNA from plasma-derived extracellular vesicles (EVs) as a minimally invasive method for detecting clinically significant somatic mutations in cancer patients. It compares somatic variants in tumor tissue with those in matched plasma EV DNA across brain, colorectal, and thyroid cancers, demonstrating that EV DNA can identify unique pathogenic variants not detected in cell-free DNA (cfDNA), highlighting its promise as a complementary tool in liquid biopsy applications.
Engineered reverse transcriptases and Taq DNA polymerases deliver robust yield in the presence of clinically relevant inhibitors
PCR/qPCR RT-PCR/RT-qPCR DNA RNA Enzymes MDx StellarScript StellarScript HT StellarScript HT+ StellarTaqThis poster discusses the engineering of reverse transcriptases and Taq DNA polymerases to enhance thermostability and inhibitor tolerance, addressing challenges in molecular diagnostics. The engineered enzymes, such as StellarScript HT+ and aCat174 Taq DNA polymerase, demonstrate improved performance in the presence of common inhibitors, making them suitable for applications like RT-qPCR, RNA sequencing, and PCR amplification from challenging samples.
Evaluation of library amplification systems for high stringency applications
Illumina DNA DNA NGS EquinoxThis poster evaluates the Equinox Library Amplification Kit's performance in high-stringency applications, emphasizing its efficiency across a broad range of GC contents (20.8% to 80.9%) and its ability to amplify long library inserts without bias. The kit maintains amplification efficiency even as product accumulates, which is crucial for hybridization capture workflows. Additionally, Equinox generates uniform Unique Molecular Index (UMI) families, enhancing sequencing economy and error correction. It also exhibits excellent fidelity and near-complete hot start inhibition of both polymerase and exonuclease activities, making it suitable for automated library amplification.
Improving data quality and reproducibility with FFPE-derived RNA using a novel, rapid whole transcriptome library prep workflow
Gene Expression WTS Illumina RNA Blood FFPE RNA NGS Polaris LPKThis 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
Fusions Gene Expression mRNA Targeted WTS Illumina RNA FFPE RNA NGS Polaris LPKThis 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.
Optimized enzymatic fragmentation workflow for the rapid construction of high-quality whole genome and whole exome libraries that is compatible with several blood collection methodologies
PCR-free WGS WGS Illumina DNA Blood Dried Blood Spot Saliva/buccal DNA NGS Frag LPKThis poster presents the Watchmaker DNA Library Prep Kit with Fragmentation, optimized for rapid, high-quality library construction from various DNA collection methods, including whole blood, buccal swabs, at-home blood collection devices (Tasso™), and dried blood spots. The workflow achieves high library conversion rates across sample types, with consistent sequencing performance and variant calling concordance. Adjusting post-ligation SPRI cleanup can further enhance performance, and tuning post-ligation size selection allows for larger insert libraries.
Overcoming sample quality and quantity limitations for NGS analysis of clinically relevant samples
Liquid Biopsy Targeted WGS DNA FFPE Plasma/cfDNA DNA NGS DNA LPK Frag LPKThis poster addresses challenges in next-generation sequencing (NGS) of clinically relevant samples, specifically cell-free DNA (cfDNA) and formalin-fixed, paraffin-embedded (FFPE) tissues, which often suffer from limited quantity and quality. It highlights how Watchmaker Genomics' innovative library preparation kits enhance scalability and sensitivity, enabling high-quality library construction from these challenging samples. These advancements facilitate more accurate and reliable NGS analyses in clinical genomics.
Purpose built reverse transcriptases and Taq DNA Polymerases deliver high yield in the presence of inhibitors
PCR/qPCR RT-PCR/RT-qPCR DNA RNA Cell Line Frozen Tissue Enzymes MDx StellarScript StellarScript HT StellarScript HT+This poster discusses the engineering of reverse transcriptases (RTs) and Taq DNA polymerases (Taq DNAPs) to enhance thermostability, inhibitor tolerance, and speed. The study identifies RT variants with increased thermostability and inhibitor tolerance, and Taq DNAP variants with enhanced speed and inhibitor tolerance, making them suitable for point-of-care applications.
Scalable and flexible library preparation for high-sensitivity applications
CNV Metagenomics Variant Calling WGS Illumina Singular DNA Cell Line Microbial DNA NGS Frag LPKThis poster demonstrates the integration of Watchmaker Genomics' DNA Library Prep Kit with Fragmentation and the Singular Genomics G4™ Sequencing Platform for high-sensitivity applications. The combined workflow enables accurate copy number variation (CNV) detection and metagenomic analysis, achieving high mapping rates and low chimeric fractions across various cell lines. Sequencing results from the G4 platform align closely with those from leading NGS platforms, indicating seamless integration and reliable performance.
Generating higher quality transcriptomic data from challenging sample types
Gene Expression Automation WTS Illumina RNA RNA NGS Polaris LPKThis 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.
The use of engineered reverse transcriptase and Taq DNA polymerase variants for improved activity and inhibitor tolerance in POC MDx applications
PCR/qPCR RT-PCR/RT-qPCR DNA RNA Blood Saliva/buccal Urine MDx StellarScript HT+ StellarTaqThis poster presents data demonstrating the inhibitor tolerance of StellarTaq, including sample types such as urine, saliva and blood, purification contaminants such as heparin and DMSO, and reverse transcriptase.
Optimization of Recombinase Polymerase Amplification (RPA) highlights the importance of enzyme consistency for reproducible results
Isothermal Amp DNA Enzymes MDx RPAThis poster presents data showing how Watchmaker individual enzyme QC for RPA enzymes leads to reliable, consistent amplification. Effects of damaged proteins in RPA reactions are measured, as well as the effect of multiple freeze-thaw cycles.
PROTOCOLS
Watchmaker RNA Library Prep Kit with Polaris Depletion User Guide
DNA RNA NGS Polaris LPK 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.
Equinox Library Amplification Kits User Guide
DNA NGS RNA NGS Equinox Equinox UProtocol for Equinox® Library Amplification Kit which deliver high-efficiency, low-bias NGS library amplification with hot-start enzymes, supporting broad inputs and various sequencing applications.
phi29 DNA Polymerase Technical Guide
Enzymes phi29 DNAPProtocol for Watchmaker Genomics' phi29 DNA Polymerase Kit which offers high-fidelity, isothermal DNA amplification with strong strand displacement and high processivity, ideal for applications like multiple displacement amplification (MDA), rolling circle amplification (RCA), whole genome amplification (WGA), cell-free cloning, and DNA template preparation for sequencing.
Watchmaker DNA Library Prep Kit with Fragmentation for library construction on the Singular G4™ Platform
Singular DNA NGS Frag LPKProtocol for the Watchmaker DNA Library Prep Kit with Fragmentation, combined with Singular Genomics' G4™ Universal Adapters. This workflow offers an efficient, automation-friendly workflow for sequencing on the G4™ Platform. It integrates enzymatic fragmentation, end-repair, and A-tailing in a single reaction, minimizing bias and artifacts. The kit supports various input amounts and provides tunable insert sizes, making it suitable for multiple sequencing applications.
RNase Inhibitor Technical Guide
Enzymes MDx RNA NGS RNase InhibitorProtocol for Watchmaker Genomics' RNase Inhibitor which binds RNases A, B, and C, protecting RNA integrity in applications like RT-PCR and single-cell RNA-seq at temperatures up to 55°C.
StellarScript HT Reverse Transcriptase Kit User Guide
Enzymes MDx StellarScript HTStellarScript® HT Reverse Transcriptase enables efficient, high-specificity cDNA synthesis at 50°C, ideal for degraded RNA inputs and applications like RT-qPCR and RNA sequencing.
StellarScript HT+ Reverse Transcriptase Kit User Guide
Enzymes MDx StellarScript HT+Protocol for StellarScript® HT+ Reverse Transcriptase - an engineered M-MLV variant with enhanced thermostability and reduced RNase H activity, enabling efficient cDNA synthesis at 42°C to 65°C. It offers increased specificity, higher cDNA yields, and supports applications like RT-qPCR, primer extension, template switching, and RNA sequencing.
StellarScript Reverse Transcriptase Kit User Guide
Enzymes MDx StellarScriptProtocol for StellarScript® Reverse Transcriptase enables efficient, specific cDNA synthesis at 42°C, supporting applications like RT-qPCR and RNA sequencing with intact or degraded RNA inputs.
T4 DNA Ligase 120U/µL Technical Guide
Enzymes T4 DNA LigaseProtocol for T4 DNA Ligase (120 U/µL) efficiently joins blunt/cohesive ends and repairs nicks in DNA/RNA, ideal for cloning, adapter ligation, and molecular biology applications.
T4 DNA Ligase 600U/µL Technical Guide
Enzymes T4 DNA LigaseProtocol for T4 DNA Ligase (600 U/µL) joins blunt/cohesive DNA ends and repairs nicks, ideal for cloning, adapter ligation, and mutagenesis, with standard or rapid buffers available.
T4 DNA Polymerase Technical Guide
Enzymes T4 DNAPProtocol for T4 DNA Polymerase (3 U/µL) catalyzes 5'→3' DNA synthesis and has 3'→5' exonuclease activity, enabling gap filling and blunt-end formation for applications like library preparation.
T4 Gene 32 Protein Technical Guide
Enzymes T4 gp32Protocol for T4 Gene 32 Protein (gp32) is a single-stranded DNA-binding protein from T4 bacteriophage that stabilizes ssDNA, enhancing yields in molecular biology assays like PCR and RT-PCR.
T4 Polynucleotide Kinase Technical Guide
Enzymes T4 PNKProtocol for T4 Polynucleotide Kinase (10 U/µL) which transfers the γ-phosphate from ATP to the 5'-OH of DNA or RNA, enabling 5'-end labeling and phosphorylation for ligation. It also removes 3'-phosphates.
Taq DNA Polymerase Technical Guide
Enzymes Taq DNAPProtocol for Taq DNA Polymerase (5 U/µL), which catalyzes 5'→3' DNA synthesis and exhibits 5'→3' exonuclease activity without proofreading, ideal for PCR, qPCR, and A-tailing.
Watchmaker DNA Library Prep Kit User Guide
DNA NGS DNA LPKProtocol for Watchmaker DNA Library Prep Kit for Fragmented Double-Stranded DNA, which supports robust and flexible library preparation from fragmented DNA templates for various sequencing applications.
Watchmaker DNA Library Prep Kit with Fragmentation User Guide
DNA NGS Frag LPKProtocol for Watchmaker DNA Library Prep Kit with Fragmentation, which enables efficient conversion of DNA into Illumina®-compatible libraries through integrated enzymatic fragmentation, end-repair, and A-tailing in a single-tube reaction, minimizing bias and artifacts.
Watchmaker mRNA Library Prep Kit User Guide
RNA RNA NGS mRNA LPKProtocol for Watchmaker mRNA Library Prep Kit, which enables streamlined preparation of stranded mRNA sequencing libraries from 2.5 ng to 1000 ng of intact total eukaryotic RNA, enriching for polyadenylated mRNAs and converting them into adapter-ligated, double-stranded cDNA fragments.
Watchmaker RNA Library Prep Kit User Guide
RNA RNA NGS RNA LPKProtocol for Watchmaker RNA Library Prep Kit, which enables streamlined preparation of stranded RNA sequencing libraries from 0.25 ng to 100 ng of total or enriched RNA, accommodating both high- and low-quality samples, including FFPE material.
StellarTaq DNA Polymerase Technical Guide
Enzymes MDx StellarTaqThis protocol details the use of StellarTaq™ DNA Polymerase - engineered for speed, inhibitor tolerance, and specificity for applications like pathogen detection, qPCR, and RT-qPCR. It also describes its ability to amplify uracil-containing templates, incorporate modified bases, and perform A-tailing on DNA products.
DNA Polymerase I Technical Guide
Enzymes DNAP IProtocol for Watchmaker Genomics' DNA Polymerase I Kit which enables high-fidelity DNA synthesis, second-strand synthesis, and nick translation. Ideal for defined DNA substrates; store at -20°C.
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