Watchmaker RNA Library Prep Kit (Total RNA)
Sensitivity meets speed for total RNA.
The Watchmaker RNA Library Prep Kit turns total or previously enriched RNA into stranded, high-complexity sequencing libraries in under 3.5 hours — across an exceptionally wide input window of 0.25 ng to 100 ng. A streamlined workflow with fewer clean-up and handling steps cuts hands-on time and consumable use, while an engineered reverse transcriptase purpose-built for RNA sequencing improves conversion of RNA to cDNA, especially where template is scarce or compromised.
Engineered for the difficult sample.
Two sample types break most RNA preps: degraded material such as FFPE, and template-limited inputs such as fine-needle biopsies. A dedicated FFPE treatment step addresses the chemical damage and residual cross-linking that fixation leaves behind, while the kit's reverse transcriptase preserves complexity down to a quarter of a nanogram. The result is more clinically relevant samples made addressable — and more unique genes recovered from them.
Built to sit upstream of enrichment.
The kit works from total RNA and is designed to feed directly into downstream target enrichment and hybridisation-capture protocols, focusing sequencing on the RNAs of interest. Reduced handling and purification make it straightforward to automate on liquid-handling platforms.
- FFPE-ready: a novel treatment step improves robustness with damaged, cross-linked templates.
- Genuinely low-input: high-complexity libraries from as little as 0.25 ng total RNA.
- Enrichment-friendly: stranded total-RNA libraries built for hybrid-capture and targeted panels.
Performance data referenced on this page were generated with ribosomal and globin depletion performed upstream of library prep. For whole-transcriptome workflows with integrated rRNA/globin depletion, see the RNA Library Prep Kit with Polaris® Depletion.
For Research Use Only. Not for use in diagnostic procedures.
| Parameter | Specification |
| RNA input range | 0.25 – 100 ng of total or previously enriched RNA |
| Library type | Stranded (directional) RNA-seq |
| Turnaround time | < 3.5 hours |
| Sample compatibility | Intact and degraded RNA, including FFPE and whole blood |
| Key enzymology | Engineered RNA-seq reverse transcriptase; Equinox® DNA Polymerase |
| Typical use cases | Upstream of target enrichment / hybridisation capture configurations |
| Sequencing platforms | Illumina; compatible with Element, Singular and Ultima when combined with mRNA Capture or Polaris® Depletion modules |
| Shipping conditions | Shipped on ice packs |
| Storage conditions | −20 °C ± 5 °C |
| Shelf life | 24-rxn: ≥ 6 months · > 24-rxn: ≥ 12 months |
| Quality system | Manufactured under ISO 13485:2016 |
| Article Number | Description | Reactions |
| 7K0078-024 | Watchmaker RNA Library Prep Kit — incl. reagents for RNA library prep and amplification | 24 rxn |
| 7K0078-096 | Watchmaker RNA Library Prep Kit — incl. reagents for RNA library prep and amplification | 96 rxn |
| 7K0078-384 | Watchmaker RNA Library Prep Kit — incl. reagents for RNA library prep and amplification | 384 rxn |
| Custom fills, concentrations, packaging and private-label formats are available on request. | ||
| Topic | Detail |
| Input quality | Total or enriched RNA; high-quality through degraded (FFPE) |
| Enrichment / depletion | Compatible with downstream target enrichment; pair with depletion (e.g. Polaris®) upstream for whole-transcriptome work |
| Adapters | Watchmaker Stubby Adapters & UDI Primers available (Plate 1A, 24 indexes) |
| Long-read | Not recommended — random priming does not generate full-length cDNA |
| Non-Illumina platforms | Element, Singular, Ultima — when combined with mRNA Capture or Polaris® Depletion modules |
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A total-RNA chemistry built around degraded and template-limited inputs
Degraded & FFPE RNA
A dedicated FFPE treatment step counters fixation damage and cross-linking to recover usable data from archival blocks.
Targeted sequencing & capture
Stranded total-RNA libraries built to feed hybridisation-capture and targeted panels, focusing reads on the RNAs you care about.
Gene fusion detection
Robust conversion and even coverage support sensitive fusion detection, including from challenging clinical-research samples.
Ultra-low-input RNA
High-complexity libraries from as little as 0.25 ng — ideal for fine-needle biopsies and other precious samples.
Whole-blood RNA
Reliable complexity from whole-blood inputs when paired with upstream ribosomal/globin depletion.
Automation-friendly prep
Fewer clean-up and handling steps make the workflow straightforward to deploy on liquid handlers.
A shorter route to sequence-ready libraries
Combined steps and fewer clean-ups than other commercial kits
1. Treatment & fragment
An FFPE treatment step plus combined fragmentation and priming prepare even damaged templates for conversion.
2. Synthesise cDNA
First- and second-strand synthesis with an RNA-seq-tuned reverse transcriptase maximises RNA-to-cDNA conversion.
3. Ligate
Adapter ligation produces strand-marked, sequencing-ready fragments with minimal handling.
4. Amplify
Equinox® master mix delivers even, low-bias amplification ready for capture or direct sequencing.
- STRANDED RNA LIBRARIES IN UNDER 3.5 HOURS
- INPUTS FROM 0.25 ng
- ENGINEERED FOR FFPE
- BUILT FOR TARGET ENRICHMENT
- FEWER CLEAN-UPS, EASY TO AUTOMATE
- STRANDED RNA LIBRARIES IN UNDER 3.5 HOURS
- INPUTS FROM 0.25 ng
- ENGINEERED FOR FFPE
- BUILT FOR TARGET ENRICHMENT
- FEWER CLEAN-UPS, EASY TO AUTOMATE
Rescue data from FFPE
A treatment step built for fixed, cross-linked templates
FFPE samples are inherently hard to sequence: fixation fragments the template and leaves residual cross-linking that throttles conversion. Watchmaker's novel FFPE treatment step, paired with a reverse transcriptase engineered for RNA sequencing, restores sensitivity where it counts. Across five independent FFPE blocks prepared from 100 ng RNA, the Watchmaker workflow detected more unique genes than the comparator — turning clinically relevant but difficult archival material into a productive sequencing input.
Complexity from the smallest inputs
High-complexity libraries down to 0.25 ng
Template-limited sample types — fine-needle biopsies and similar — are difficult to process reproducibly, which directly limits the sensitivity of any assay built on top of them. The Watchmaker RNA Library Prep Kit generates high-complexity libraries from as little as 0.25 ng of RNA, maintaining unique-gene detection as input falls. More of your precious sample converts into informative, sequenceable molecules.
Accurate quantification as input drops
Preserve the expression profile across a 50-fold input change
A good library prep should report the same biology whether you start with 500 ng or 10 ng. Many kits distort the picture at low input, selectively losing low-abundance genes. Differential-expression analysis between 500 ng and 10 ng whole-blood libraries shows the Watchmaker kit better preserves the gene-expression profile, where other commercial solutions lose representation of low-abundance transcripts — giving you confidence that input variation isn't masquerading as biological signal.
Choose the right Watchmaker RNA chemistry
Three kits, one engineering philosophy — matched to your sample and question
mRNA Library Prep Kit
Poly(A)-enriched coding-transcriptome libraries from intact RNA (2.5 ng – 1 µg) in < 5 h. Best for gene expression, fusions, isoforms.
RNA Library Prep Kit (Total)
Streamlined total-RNA libraries (0.25 – 100 ng) for downstream target enrichment / hybridisation capture. Handles intact and FFPE inputs.
RNA Library Prep Kit with Polaris® Depletion
Whole-transcriptome libraries with rRNA + globin depletion in < 4.5 h from as little as 1 ng; tailored FFPE handling and lncRNA detection.
COMPLETE YOUR NGS PIPELINE
Tailored Solutions for Challenging Applications
A great result relies on more than just a single high-quality reagent. Visit our Solutions page to see how we integrate cutting-edge technologies, like Watchmaker Genomics, into end-to-end workflows designed to maximize your laboratory’s efficiency and sequencing yield.
Technical insights & kit selection
Practical guidance on matching the total-RNA chemistry to your samples and platform.
It works from 0.25 ng to 100 ng of total or previously enriched RNA, including intact, degraded and FFPE material as well as whole blood. It is designed to sit upstream of target enrichment and hybridisation capture.
Yes. It uses total RNA and is compatible with downstream target enrichment to focus sequencing on RNAs of interest. To remove uninformative transcripts without target enrichment, use the mRNA Library Prep Kit (poly(A)) or the RNA Library Prep Kit with Polaris® Depletion (rRNA/globin).
A dedicated FFPE Treatment Buffer addresses the chemical damage and cross-linking introduced by fixation, and the engineered reverse transcriptase improves conversion — together recovering high-complexity libraries from samples that typically fail with standard RT enzymes.
Illumina by default, and the kit has been demonstrated compatible with Element, Singular and Ultima when combined with the mRNA Capture or Polaris® Depletion modules.
Yes. Fewer clean-up and handling steps reduce hands-on time, and 96-reaction kits include generous overages for liquid-handler dead volumes. Ask us about scripts for your platform.
Yes. The workflow produces directional, stranded RNA-seq libraries.
No. Random priming during first-strand synthesis does not generate full-length cDNA, so it is not recommended for native long-read applications.
Yes. Watchmaker's quality management system is certified to ISO 13485:2016 for the design, development and manufacture of reagents for genomics applications in medical research.