Sensitivity meets Speed
Watchmaker RNA Library Prep Kits deliver stranded, high-complexity RNA-seq libraries in under 3.5 hours with inputs ranging from 0.25 to 100 ng total RNA.
The easily automated workflow saves time and reduces consumable use by incorporating fewer cleanup and handling steps. Performance with low-input and degraded samples is improved by the incorporation of a novel, engineered reverse transcriptase.
Key Features and Benefits
- A novel treatment step improves robustness with challenging FFPE samples
- The rapid, streamlined workflow generates stranded, high-quality libraries in under 3.5 hours
- Reduced handling and purification steps enhance automatability
- A reverse transcriptase engineered specifically for RNA sequencing improves conversion of RNA to cDNA
Applications
- RNA sequencing with degraded samples, such as FFPE
- Targeted sequencing protocols employing hybridization capture
- Gene fusion detection
Streamlined, automatable workflow
Figure 1. A simple, rapid workflow for scalable sample processing. The Watchmaker RNA Library Prep Kit combines and shortens reaction steps and has fewer cleanups than other commercially available kits.
Key Performance Data
A solution designed with FFPE samples in mind
FFPE samples are inherently challenging to process due to template damage and residual cross-linking. Watchmaker’s novel FFPE treatment step, paired with a reverse transcriptase engineered for RNA sequencing, provides highly sensitive performance and makes more clinically relevant samples addressable.
Data shown were generated with ribosomal and globin depletion upstream of library prep. Learn more about the Watchmaker RNA Library Prep Kit with Polaris® Depletion.
A solution designed with FFPE samples in mind
Improve sensitivity with low-input samples
Template-limited sample types, such as fine needle biopsies, can be difficult to process robustly and reproducibly — limiting the sensitivity of associated assays. The Watchmaker RNA Library Prep Kit generates high-complexity libraries with as little as 0.25 ng of RNA.
Data shown were generated with ribosomal and globin depletion upstream of library prep. Learn more about the Watchmaker RNA Library Prep Kit with Polaris Depletion.
Improve sensitivity with low-input samples
Accurately quantify gene expression 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. 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.
Data shown were generated with ribosomal and globin depletion upstream of library prep. Learn more about the Watchmaker RNA Library Prep Kit with Polaris Depletion.
Figure 4. Prevent data distortion with ... MORE
Accurately quantify gene expression 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 with the vendor-specific ribosomal and globin depletion kit employed upstream of library prep. Data were randomly downsampled to 16M paired reads per library. Differential expression analysis between averaged 500 ng (control) and 10 ng (test) 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.
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.
mRNA Library Prep Kit Brochure
Fusion Detection Gene Expression Analysis Isoform Detection/Alternative Splicing Long Noncoding RNA Analysis mRNA Sequencing Novel Transcript Discovery SNV/SNP/InDel Detection Element Illumina Singular Ultima RNA Blood Dried Blood Spot RNA NGS mRNA Library Prep RNA Library PrepThe 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.
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.
PROTOCOLS
Watchmaker RNA Library Prep Kit User Guide
RNA RNA NGS RNA Library PrepProtocol 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.
| RNA input range | 0.25 - 100 ng of previously enriched or total RNA |
|---|---|
| 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 |
Is this kit compatible with RNA enrichment or depletion?
The RNA Library Prep Kit utilized total RNA and is compatible with downstream target enrichment, to focus sequencing on RNAs of interest.
To remove uninformative transcripts without the need for target enrichment, consider the Watchmaker mRNA Library Prep Kit or RNA Library Prep Kit with Polaris® Depletion.
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 with Polaris Depletion removes uninformative ribosomal and globin RNAs allowing for whole transcriptome analysis. This kit is compatible with both high quality and degraded RNA samples.
The Watchmaker RNA Library Prep Kit utilized total RNA and is compatible with downstream target enrichment, to focus sequencing on RNAs of interest.
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 when combined with the mRNA Capture or Polaris Depletion modules.
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.
Not seeing the full table? Rotate your phone to view in landscape mode.
| Description | 24 rxn | 96 rxn | 384 rxn | |
|---|---|---|---|---|
| Watchmaker RNA Library Prep Kit incl. reagents required for RNA library prep and amplification | 7K0078-024 | 7K0078-096 | 7K0078-384 | Request a quote |
Please contact sales@watchmakergenomics.com to inquire about custom kit configurations.
Validate your login