Product Description
LIGHT LABS is proud to offer the Zymo Research Zymo-Seq RiboFree® Total RNA Library Kit (Cat # R3003) — the premier total RNA-Seq library preparation kit available, combining the simplest workflow, the most universal rRNA depletion chemistry, and complete scalability in a single all-inclusive 96-prep kit. The Zymo-Seq RiboFree® kit is purpose-built for researchers requiring high-quality, stranded, rRNA-depleted total RNA-Seq libraries from any organism in the fastest, simplest, and most automation-friendly workflow available — achieving RNA to indexed library in as little as 3.5 hours.
The defining innovation of the Zymo-Seq RiboFree® Total RNA Library Kit is its RiboFree® Universal Depletion technology — a novel, probe-free rRNA depletion approach that is fundamentally different from all probe-based depletion methods on the market. Instead of using organism-specific probes to capture and remove rRNA sequences (which require purchasing different probe sets for different organisms and introduce probe-related off-target depletion artifacts), RiboFree® Universal Depletion uses the input RNA itself as a template to drive the enzymatic removal of reverse-transcribed cDNA from the abundant ribosomal RNA sequences. This probe-free approach is inherently universal — compatible with total RNA from any organism, including bacteria, fungi, plants, animals, and mixed-organism samples — without the need to select, design, or add organism-specific probes.
A second critical simplification in the Zymo-Seq RiboFree® workflow is simultaneous dual-adapter ligation — both P7 and P5 partial adapters are ligated to the first-strand cDNAs in a single step, without adding extra artificial sequences, dramatically reducing the number of protocol steps and hands-on time vs. sequential adapter ligation methods. Reagents throughout the protocol are provided in premixed formats ready for use. Libraries are stranded and compatible with all Illumina® sequencing platforms. LIGHT LABS is your trusted source for Zymo Research products.
KEY FEATURES
- RiboFree® Universal Depletion — probe-free rRNA depletion technology; uses input RNA as template for enzymatic removal of rRNA cDNA sequences; compatible with total RNA from ANY organism without organism-specific probes
- No probe sets required — eliminates the cost, lead time, and off-target effects of probe-based rRNA depletion; one kit, any organism; minimal off-target effects as low as 1.8% in protein-coding transcripts
- Simplest total RNA-Seq library prep — simultaneous dual-adapter ligation of both P7 and P5 adapters to first-strand cDNA in one step; premixed reagent formats throughout protocol
- 3.5 hour protocol — from RNA input to indexed library; fastest total RNA-Seq library prep available
- 10–250 ng total RNA input — optimized input range; below 10 ng possible with protocol modifications (see Appendix D)
- Stranded libraries — Read 1 sequence is antisense to RNA molecule of origin; provides strand information for accurate gene expression analysis and antisense RNA detection
- Compatible with all Illumina® sequencing platforms
- Automation-friendly streamlined protocol — suitable for liquid handling automation at 96-prep scale
- 96-prep kit — highest-volume format; best per-prep economy; ideal for core facilities and high-throughput RNA-Seq workflows
- Requires: thermocycler with heated lid, magnetic stand for 0.2 mL PCR tubes, microcentrifuge
- Storage temperature: -80°C
- Genesee Scientific Catalog No. 11-643B
- Made in the USA by Zymo Research
SPECIFICATIONS
| Attribute | Detail |
|---|---|
| Catalog Number | R3003 |
| Genesee Scientific Catalog No. | 11-643B |
| Brand | Zymo Research |
| Kit Name | Zymo-Seq RiboFree® Total RNA Library Kit |
| Number of Preps | 96 |
| rRNA Depletion Method | RiboFree® Universal Depletion — probe-free, enzymatic |
| Organism Compatibility | Universal — any organism; no organism-specific probes required |
| RNA Input Range | 10–250 ng total RNA (optimized); <10 ng with modifications |
| Library Type | Stranded total RNA-Seq |
| Adapter Ligation | Simultaneous dual-adapter ligation (P7 + P5 in one step) |
| Sequencing Compatibility | All Illumina® sequencing platforms |
| Processing Time | ~3.5 hours (RNA to indexed library) |
| Off-Target Effects | As low as 1.8% in protein-coding transcripts |
| Read Orientation | Read 1 antisense to RNA molecule of origin |
| Equipment Required | Thermocycler with heated lid; magnetic stand (0.2 mL PCR tubes); microcentrifuge; benchtop vortex |
| Storage Temperature | -80°C |
| Shipping Temperature | Room temperature & dry ice |
PROBE-FREE vs. PROBE-BASED rRNA DEPLETION
| Feature | RiboFree® Universal Depletion (R3003) | Probe-Based Depletion |
|---|---|---|
| Organism Specificity | Universal — any organism | Organism-specific probe sets required |
| Probe Cost | None — no probes needed | Additional probe purchase required per organism |
| Off-Target Effects | As low as 1.8% | Higher risk of probe off-target depletion |
| Mixed-Organism Samples | Compatible | Requires multiple probe sets |
| Workflow Complexity | One kit, any sample | Multiple kits/probe sets for different organisms |
APPLICATIONS
- Total RNA-Seq from any organism — bacteria, fungi, plants, animals, parasites, mixed-organism samples
- Whole transcriptome analysis requiring rRNA depletion without organism-specific probes
- Transcriptomics from non-model organisms where probe sets are unavailable
- Host-pathogen dual RNA-Seq requiring universal depletion of both host and pathogen rRNA
- Metatranscriptomics from mixed-organism environmental samples
- Long non-coding RNA (lncRNA) and antisense RNA profiling (stranded libraries)
- High-throughput core facility RNA-Seq library preparation at 96-prep scale
- Automation-compatible total RNA-Seq library prep workflows
- Any total RNA-Seq application requiring the fastest, simplest, most universal rRNA depletion
ORDERING INFORMATION — ZYMO RESEARCH ZYMO-SEQ RIBOFREE® TOTAL RNA LIBRARY KIT
| Cat # | Description | Preps |
|---|---|---|
| R3003 | Zymo-Seq RiboFree® Total RNA Library Kit | 96 |
| R3000 | Zymo-Seq RiboFree® Total RNA Library Kit | 12 |
| R3001 | Zymo-Seq RiboFree® Universal cDNA Kit | 12 |
| D3096 | Zymo-Seq™ UDI Primer Plate (Indexes 1–96) | 96 Indexes |
| D3008 | Zymo-Seq™ UDI Primer Set (Indexes 1–12) | 12 Indexes |
| R3008 | Zymo-Seq SwitchFree 3′ mRNA Library Kit | 12 |
| R3009 | Zymo-Seq SwitchFree 3′ mRNA Library Kit | 96 |
