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Direct RNA Sequencing Kit

A sequencing kit optimised for sequencing native RNA with improved output and accuracy.

This is an Early Access product.

Product lead time: 1 week

2Early Access
  • Access the latest products from Oxford Nanopore Technologies
  • Provide feedback into the innovation team as the product develops
  • Product Warranty may initially be limited to 1 month as it is so new
  • Product routinely iterates as new features and capabilities are added
  • Estimated lead time in store
  • Product subject to availability


This kit is highly recommended for users who:

  • Would like to remove PCR bias
  • Are exploring attributes of native RNA such as modified bases

Please note that to use this kit, you will need to purchase additional 3rd party reagents: see the "3rd Party Materials" tab for more detail.

The Direct RNA Sequencing Kit features:

Preparation time135 minutes
Input requirement300 ng poly(A)+ RNA or 1 μg total RNA
PCR requiredNo
Read lengthRNA length
Associated protocolsDirect RNA sequencing (SQK-RNA004)
Direct RNA sequencing - control experiment (SQK-RNA004)
Direct RNA sequencing - sequence-specific (SQK-RNA004)
Pack size6 reactions
StabilityShipped at 2–8°C

Long-term storage -20 – -30°C

The warranty for this Early Access product is 3 months from receipt by the customer

The Direct RNA Sequencing Kit (SQK-RNA004) is used to prepare and sequence native RNA without conversion to cDNA. Inputs include poly(A)-tailed RNA or total RNA, such as eukaryotic mRNA and viral RNA.

This kit upgrade includes increased sequencing output and improved modal raw read accuracy on our new RNA flow cell (FLO-MIN004RA and FLO-PRO004RA). The flow cell priming reagents are also included as part of the sequencing kit and have been reformulated to be compatible on the new RNA flow cell. Other updates include fuel fix technology, allowing users to run longer experiments without the need for fuel addition during the run.

Further considerations:

In applications where Direct RNA sequencing’s key advantages (detection of modified bases and reduced bias) are not important, users may consider one of Oxford Nanopore’s cDNA kits which currently provide the highest output per run.

Shipping and logistics:

Flow cells and kits are shipped together in an environmentally friendly temperature-controlled shipping box.

Products are shipped to customers within the USA and EU Monday to Thursday. Shipments to Canada, Norway, Korea and Japan are expedited Monday to Wednesday; with Australia and New Zealand leaving our warehouses on a Friday. Shipments to the rest of the world are made on Mondays to allow the full working week for packages to arrive.

The delivery charges are calculated when a quote is raised or during checkout. Once an order is made, the delivery ID and delivery information can be tracked in the Store.


The Direct RNA Sequencing Kit (SQK-RNA004) is used to prepare either poly(A)-tailed RNA or total RNA for sequencing by performing reverse transcription to synthesise a secondary complementary cDNA strand for stability to improve sequencing output. Sequencing adapters are then attached to the RNA-cDNA hybrid for sequencing.

Direct RNA004 workflow

What's in the box

The Direct RNA Sequencing Kit contains enough reagents for six reactions.

SQK-RNA004 tubes

NameAcronymCap colourNo. of vialsFill volume per vial (μl)
RT AdapterRTABlue110
RNA Ligation AdapterRLAGreen145
RNA CSRCSYellow125
Wash BufferWSBOrange21,200
RNA Elution BufferREBBlack1300
Library SolutionLISWhite cap, pink label1600
Sequencing BufferSBRed1700
RNA Flush TetherRFTPink1200
Flow Cell FlushFCFClear cap, light blue label18,000

Note: The RNA CS (RCS) is the calibration strand and contains the Enolase II from YHR174W, extracted from the yeast saccharomyces cerevisiae. The reference FASTA files for the yeast is available here.

3rd party materials


  • 1.5 ml Eppendorf DNA LoBind tubes
  • 0.2 ml thin-walled PCR tubes
  • Nuclease-free water (e.g. ThermoFisher, AM9937)
  • Freshly prepared 70% ethanol in nuclease-free water
  • SuperScript™ III Reverse Transcriptase (Thermo Fisher Scientific, 18080044)
  • 10 mM dNTP solution (e.g. NEB N0447)
  • NEBNext® Quick Ligation Reaction Buffer (NEB, B6058)
  • T4 DNA Ligase 2M U/ml (NEB, M0202T/M)
  • RNaseOUT™, 40 U/μl (Life Technologies, 10777019)
  • Agencourt RNAClean XP beads (Beckman Coulter™, A63987)
  • Qubit RNA HS Assay Kit (ThermoFisher Q32852)
  • Qubit dsDNA HS Assay Kit (ThermoFisher, cat # Q32851)
  • Qubit™ Assay Tubes (Invitrogen, Q32856)


  • Hula mixer (gentle rotator mixer)
  • Magnetic separator, suitable for 1.5 ml Eppendorf tubes
  • Microfuge
  • Vortex mixer
  • Ice bucket with ice
  • Timer
  • Thermal cycler
  • Qubit fluorometer (or equivalent for QC check)
  • P1000 pipette and tips
  • P200 pipette and tips
  • P100 pipette and tips
  • P20 pipette and tips
  • P10 pipette and tips
  • P2 pipette and tips
  • Eppendorf 5424 centrifuge (or equivalent)

Note: The above are 3rd party reagents required for the standard prep. For other workflows using this kit, extra 3rd party reagents may be required.


The Direct RNA Sequencing Kit can be used together with:


  • Flow Cell Wash Kit (EXP-WSH004)

Note: The Flow Cell Wash Kit (EXP-WSH004) can be used to remove library between flow cell washes and library re-loading. Please note, this kit is not compatible with RNA as a nuclease wash.

Flow cells

  • FLO-MIN004RA
  • FLO-PRO004RA


  • MinION Mk1B
  • MinION Mk1C
  • GridION
  • PromethION