Watchmaker mRNA Library Prep Kit
A focused view of the coding transcriptome.
The Watchmaker mRNA Library Prep Kit builds stranded, high-complexity mRNA-seq libraries from intact eukaryotic RNA in under five hours — comfortably inside a single working day. Poly(A) selection concentrates your sequencing budget on the messenger RNA you actually want to measure, so every read counts toward biological insight rather than ribosomal background.
One workflow across a 400-fold input range.
A single, flexible protocol spans 2.5 ng to 1 µg of total RNA, removing the need to switch to a separate low-input chemistry that sacrifices strand information. At the demanding end of that range, the kit's engineered reverse transcriptase and high-efficiency library construction preserve library complexity where other kits collapse — detecting more unique genes from precious, template-limited samples while delivering equivalent performance when input is not limiting.
Designed to be automated, not just compatible.
Combined and shortened reaction steps, fewer clean-ups and "on-magnet" bead washing during mRNA capture cut hands-on time and consumable use. Generous reagent overages on the 96-reaction format absorb the dead volumes of liquid-handling platforms, so the same protocol scales from a handful of samples to full-plate throughput.
- Stranded by design: directional libraries preserve strand-of-origin information for confident antisense and overlapping-transcript interpretation.
- Engineered enzymology: a reverse transcriptase tailored for RNA sequencing improves RNA-to-cDNA conversion; Equinox® DNA Polymerase amplifies GC-rich regions evenly.
- Broad platform reach: validated on Illumina and demonstrated compatible with Element, Singular and Ultima short-read platforms.
For Research Use Only. Not for use in diagnostic procedures.
| Parameter | Specification |
| RNA input range | 2.5 ng – 1 µg of intact total eukaryotic RNA (RIN > 7) |
| Library type | Stranded (directional) mRNA-seq |
| Turnaround time | < 5 hours |
| Enrichment | Poly(A) capture (on-magnet bead washing) |
| Key enzymology | Engineered RNA-seq reverse transcriptase; Equinox® DNA Polymerase |
| mRNA Capture Kit contents | mRNA Capture Beads · Bead Prep Buffer · Capture Buffer · Final Wash Buffer |
| 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) |
| Sample compatibility | Eukaryotic, intact RNA from tissues and cell lines; not for degraded/FFPE inputs |
| Sequencing platforms | Illumina; demonstrated compatible with Element, Singular, Ultima |
| Shipping conditions | Ice packs |
| Storage | mRNA Capture Kit: 2–8 °C · RNA Library Prep Kit: −25 to −15 °C (−20 °C ± 5 °C) |
| Shelf life | ≥ 6 months upon receipt |
| Quality system | Manufactured under ISO 13485:2016 |
| The FFPE Treatment Buffer supplied in the RNA Library Prep module is **not used** in the mRNA workflow and may be set aside. | |
| Article Number | Description | Reactions |
| 7BK0001-024 | Watchmaker mRNA Library Prep Kit — incl. reagents for mRNA capture, RNA library prep and amplification | 24 rxn |
| 7BK0001-096 | Watchmaker mRNA Library Prep Kit — incl. reagents for mRNA capture, RNA library prep and amplification | 96 rxn |
| 7BK0001-384 | Watchmaker mRNA Library Prep Kit — incl. reagents for mRNA capture, RNA library prep and amplification | 384 rxn |
| The mRNA Library Prep Kit (7BK0001) ships as two boxes: the mRNA Capture Kit (7K0105) and the RNA Library Prep Kit (7K0078). Custom fills, concentrations and private-label formats are available on request. | ||
| Topic | Detail |
| Species | Eukaryotic (poly(A)-selected) |
| Input quality | Intact RNA, RIN > 7; free of contaminating DNA, salts, chelators and organics |
| Adapters | Requires adapters with a 3′ T-overhang; ensure adequately duplexed and at correct concentration |
| Long-read | Not recommended — random priming does not generate full-length cDNA |
| Non-coding RNA | Not detected (use the Polaris® Depletion kit for whole-transcriptome / lncRNA) |
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One stranded mRNA chemistry, validated across the applications that matter most
Gene expression analysis
Quantitative, strand-aware profiling that stays faithful to your sample from bulk down to low-input material.
Gene fusion detection
Directional libraries and even coverage help resolve fusion breakpoints in research oncology workflows.
Isoform & alternative splicing
Uniform transcript coverage supports confident isoform-level and splice-junction analysis.
Novel transcript discovery
High library complexity surfaces lowly expressed and previously unannotated coding transcripts.
SNV detection
High-fidelity amplification and even coverage underpin accurate variant calling in expressed regions.
Pathway analysis
Reproducible, undistorted expression values give downstream pathway and enrichment analyses a trustworthy foundation.
A workflow engineered for the modern lab
Fewer steps, fewer clean-ups, ready for the deck
1. Capture
Poly(A) selection enriches messenger RNA using on-magnet bead washing — no resuspension pipetting, less magnet time.
2. Fragment & synthesise
Combined fragmentation, priming and first-/second-strand synthesis with an RNA-seq-tuned reverse transcriptase.
3. Ligate
Adapter ligation prepares strand-marked, sequencing-ready fragments with minimal handling.
4. Amplify
Equinox® master mix delivers even amplification, including GC-rich regions, in fewer cycles.
- STRANDED mRNA LIBRARIES IN UNDER 5 HOURS
- 400-FOLD INPUT RANGE — 2.5 ng TO 1 µg
- ENGINEERED FOR AUTOMATION
- MORE GENES FROM LOW-INPUT SAMPLES
- EVEN COVERAGE ACROSS GC-RICH REGIONS
- STRANDED mRNA LIBRARIES IN UNDER 5 HOURS
- 400-FOLD INPUT RANGE — 2.5 ng TO 1 µg
- ENGINEERED FOR AUTOMATION
- MORE GENES FROM LOW-INPUT SAMPLES
- EVEN COVERAGE ACROSS GC-RICH REGIONS
More signal from low-input samples
Complexity where other kits collapse
Library-prep efficiency normally falls away as template becomes limiting, throttling complexity and starving downstream analysis of usable genes. The Watchmaker mRNA Library Prep Kit is optimised for exactly this regime: in a head-to-head on breast-tissue RNA (RIN 7), it detected significantly more unique genes than KAPA mRNA HyperPrep and NEBNext® Ultra™ II Directional at low inputs — and matched them when RNA was abundant, on a markedly simpler workflow. At 2.5 ng, the KAPA workflow failed to produce libraries at all; Watchmaker did not.
Spend your reads where they matter
Higher mRNA enrichment, fewer wasted bases
Residual ribosomal RNA and duplicate reads quietly erode the value of every sequencing run. Efficient poly(A) capture across the full 2.5 ng – 1 µg range keeps residual rRNA low, while high library-prep efficiency minimises PCR duplicates — so a greater share of each flow cell is spent on informative, unique coding reads. The net effect is better sequencing economy: more biology per gigabase, fewer reads thrown away.
Expression data you can trust at any input
Quantitative accuracy that holds as input drops
The goal of transcriptome sequencing is a faithful picture of the biology in the tube. Many mRNA preps distort that picture as input falls, selectively losing low-abundance genes so the output no longer represents the sample. Differential-expression analysis between 100 ng and 10 ng libraries shows the Watchmaker kit retains representation of low-abundance transcripts and reports fewer spurious differentially expressed genes — strong agreement across a 10-fold change in input. Coverage uniformity stays consistent across inputs, and Equinox® DNA Polymerase improves coverage of GC-rich regions such as exon 1 of SLC2A4RG.
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 mRNA chemistry to your samples and platform.
Intact eukaryotic total RNA (RIN > 7) from 2.5 ng to 1 µg, derived from tissues or cell lines and suspended in RNase-free water. It is not intended for degraded or FFPE material — use the RNA Library Prep Kit with Polaris® Depletion for those inputs. For amounts outside this range, contact our team.
Poly(A) capture focuses sequencing on coding transcripts. If your study only needs coverage of the coding transcriptome, mRNA enrichment improves sequencing economy by concentrating reads on the transcripts you care about. If you need ribosomal/globin removal or non-coding RNA, choose Polaris® Depletion.
Yes. The workflow produces directional, stranded mRNA-seq libraries that preserve strand-of-origin information.
Yes — it was developed with automation in mind. On-magnet washes and fewer clean-up steps reduce handling, and 96-reaction kits include generous overages for liquid-handler dead volumes. Application notes exist for Revvity Sciclone® G3 NGSx and SPT Labtech firefly®; ask us about your platform.
The kit is validated on Illumina and has been demonstrated compatible with Element, Singular and Ultima short-read platforms.
No. First-strand synthesis uses random priming and does not generate full-length cDNA, so the kit is not recommended for native long-read applications.
The mRNA Library Prep Kit (7BK0001) ships as two boxes — the mRNA Capture Kit (7K0105) and the RNA Library Prep Kit (7K0078). The FFPE Treatment Buffer in the library-prep box is not used in the mRNA workflow.
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.