Watchmaker RNA Library Prep Kit with Polaris® Depletion
The whole transcriptome, minus the noise.
The Watchmaker RNA Library Prep Kit with Polaris® Depletion builds stranded, whole-transcriptome libraries while removing the highly abundant transcripts that waste sequencing capacity. The streamlined Polaris Depletion module clears ribosomal RNA and globin mRNA from human, mouse and rat samples, redirecting reads toward the biology that matters — coding transcripts and the long non-coding RNAs that conventional poly(A) capture leaves behind.
Built for the difficult sample, fast.
A novel engineered reverse transcriptase drives efficient RNA-to-cDNA conversion across a broad 1 ng to 1 µg input range, including FFPE-derived RNA. A dedicated FFPE treatment step addresses the template damage and cross-linking left by fixation, so archival and template-limited material becomes a productive input rather than a failed run. Complete libraries — depletion included — assemble in under 4.5 hours.
One process instead of many.
Fewer bead purifications and reaction steps consolidate what used to be several niche, sample-specific workflows into a single automation-friendly protocol — cutting up to an hour of hands-on time and roughly a thousand pipette tips per plate.
- Whole-transcriptome view:** rRNA + globin depletion retains coding and long non-coding RNA (e.g. MALAT1), unlike poly(A) capture.
- FFPE- and low-input-ready:** sensitive performance from 1 ng and from degraded, fixed material.
- Consolidated & automatable:** one workflow, fewer steps, validated on multiple liquid handlers.
Globin depletion is human-only; rRNA depletion covers human, mouse and rat (HMR). For Research Use Only. Not for use in diagnostic procedures.
| Parameter | Specification |
| RNA input range | 1 ng – 1 µg of total RNA |
| Library type | Stranded (directional) whole-transcriptome |
| Depletion targets | rRNA (human, mouse, rat) + globin mRNA (human only) |
| Turnaround time | < 4.5 hours (including depletion) |
| Sample compatibility | High-quality and degraded RNA, including FFPE and whole blood |
| Key enzymology | Engineered RNA-seq reverse transcriptase; Equinox® DNA Polymerase |
| Sequencing platforms | Illumina; demonstrated compatible with Element, Singular, Ultima |
| Shipping conditions | 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 |
| 7BK0002-024 | Watchmaker RNA Library Prep Kit with Polaris® Depletion — incl. reagents for rRNA and globin depletion, RNA library prep and amplification | 24 rxn |
| 7BK0002-096 | Watchmaker RNA Library Prep Kit with Polaris® Depletion — incl. reagents for rRNA and globin depletion, RNA library prep and amplification | 96 rxn |
| 7BK0002-384 | Watchmaker RNA Library Prep Kit with Polaris® Depletion — incl. reagents for rRNA and globin depletion, RNA library prep and amplification | 384 rxn |
| Custom fills, concentrations, packaging and private-label formats are available on request. | ||
| Topic | Detail |
| Species (depletion) | rRNA: human, mouse, rat · globin: human only |
| Transcripts captured | Coding RNA + long non-coding RNA (rRNA/globin removed) |
| Coding-only alternative | Use the mRNA Library Prep Kit (poly(A)) for coding-only sequencing |
| 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 |
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Consolidate niche, sample-specific protocols into a single rapid process
Degraded & FFPE RNA
A dedicated FFPE treatment step plus depletion recovers high-complexity whole-transcriptome data from fixed, cross-linked archival material.
Long non-coding RNA
rRNA/globin depletion retains lncRNAs such as MALAT1 that poly(A) capture omits — opening up regulatory biology.
Gene fusion & splice variants
Even, full-length-transcript coverage supports sensitive fusion, splice-variant and isoform detection from challenging samples.
Gene expression analysis
Quantitative, strand-aware expression profiling that stays faithful across a wide input range.
Novel transcript discovery
High library complexity surfaces lowly expressed and previously unannotated transcripts across the whole transcriptome.
SNV detection & targeted capture
Compatible with hybridisation-capture protocols and high-fidelity variant calling in expressed regions.
Depletion and library prep, consolidated
Fewer purifications, fewer reagent additions, more walk-away time
1. Deplete
The Polaris module removes rRNA and globin mRNA (HMR) in a streamlined step, focusing reads on informative transcripts.
2. Treat & synthesise
An FFPE treatment step plus an RNA-seq-tuned reverse transcriptase convert even damaged templates efficiently.
3. Ligate
Adapter ligation produces strand-marked, sequencing-ready fragments with minimal handling.
4. Amplify
Equinox® master mix delivers even, low-bias amplification, including GC-rich regions, in fewer cycles.
- WHOLE-TRANSCRIPTOME LIBRARIES IN UNDER 4.5 HOURS
- rRNA + GLOBIN DEPLETION BUILT IN
- FROM 1 ng, INCLUDING FFPE
- SEES THE lncRNAs poly(A) MISSES
- ~1,000 FEWER TIPS PER PLATE
- WHOLE-TRANSCRIPTOME LIBRARIES IN UNDER 4.5 HOURS
- rRNA + GLOBIN DEPLETION BUILT IN
- FROM 1 ng, INCLUDING FFPE
- SEES THE lncRNAs poly(A) MISSES
- ~1,000 FEWER TIPS PER PLATE
More from FFPE than any other workflow
Closer to fresh-frozen truth, from fixed tissue
Fixation fragments RNA and leaves residual cross-linking, so the real test of an FFPE workflow is how much of the fresh-frozen signal it recovers. On a matched fresh-frozen/FFPE sample set at just 10 ng, the Watchmaker kit recovered a significantly higher percentage of the genes seen in the fresh-frozen control than KAPA RNA HyperPrep with RiboErase, NEBNext Ultra II Directional with depletion, and Illumina Stranded Total RNA with Ribo-Zero Plus — and detected more unique genes in both sample types. More of your archival cohort becomes usable, comparable data.
Sensitivity down to 1 ng
High-complexity whole-transcriptome libraries from template-limited samples
When RNA is scarce — fine-needle biopsies, micro-dissected tissue — robust, reproducible prep is the limiting factor for assay sensitivity. The Polaris workflow generates high-quality libraries from as little as 1 ng, detecting more unique genes at low input than comparator workflows and wasting fewer bases to rRNA and globin as input drops. The result is better sequencing economy exactly where every read counts.
Sequence blood efficiently — and see the lncRNAs
Remove globin and rRNA, keep the regulatory transcriptome
In blood, globin mRNA alone can claim 30% or more of your reads, and poly(A) capture quietly discards a large fraction of long non-coding RNAs. Polaris Depletion clears both rRNA and globin mRNA while preserving lncRNA coverage — including MALAT1, implicated in at least 17 cancer types — with strong coverage even across its GC-rich regions. You spend reads on informative exonic and non-coding transcripts instead of background.
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 Polaris whole-transcriptome chemistry to your samples and platform.
It depletes ribosomal RNA across human, mouse and rat (HMR) and globin mRNA in human samples. Both coding RNA and long non-coding RNA remain represented in the sequencing data.
Yes. Because it depletes rather than poly(A)-selects, the data include both coding and long non-coding transcripts. If you only need coding transcripts, the mRNA Library Prep Kit (poly(A)) is the more economical choice.
Illumina by default, with demonstrated compatibility on Element, Singular and Ultima.
Globin mRNA can consume 30% or more of reads in blood, and poly(A) capture omits many lncRNAs. Polaris removes rRNA and globin while preserving lncRNA coverage, improving sequencing economy and biological insight.
Complete libraries — including depletion — assemble in under 4.5 hours. Fewer purifications and reagent additions save up to ~1 hour and ~1,000 pipette tips per plate versus other kits.
Yes. It was designed for automation, with generous overages on 96-reaction kits. Validated application notes exist for Beckman Biomek i7, Revvity Sciclone G3 NGSx, Hamilton Microlab NGS STAR and Eppendorf epMotion 5075t — ask us about your platform.
1 ng to 1 µg of total RNA, including high-quality, degraded and FFPE material as well as whole blood. A dedicated FFPE treatment step handles fixation damage.
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.