NCM 2023: Houston
  17th - 19th May
Direct RNA Sequencing Kit

Sequence RNA molecules directly and preserve base modifications.

This uses Kit 9 chemistry.

Includes a Flow Cell Priming Kit

This product is scheduled to be discontinued in March 2024 and removed from the store January 2024. The recommended replacement is SQK-RNA004

  • These Products are nearing their end of life and will soon be discontinued
  • Users need to contact customer support to discuss project completion timelines
  • Warranty periods of 3 months or more
  • Product discontinuation within 3-6 months
  • Lead time visible in store
  • Product subject to availability


This kit is highly recommended for users who:

  • Would like to remove RT or PCR bias
  • Have transcripts that are difficult to reverse transcribe
  • 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 time105 minutes
Input requirement500 ng total RNA or 50 ng poly(A)+ RNA
Reverse transcription requiredOptional
PCR requiredNo
Read lengthEqual to RNA length
Kit chemistryKit 9
Typical number of reads1 million full-length per flow cell on MinION/GridION; 8 million per flow cell on PromethION
Associated protocolsDirect RNA sequencing - control experiment (SQK-RNA002)
Direct RNA sequencing (SQK-RNA002)
Direct RNA sequencing - sequence-specific (SQK-RNA002)
Multiplexing optionsFlow Cell Wash Kit
Pack size6 reactions
StabilityShipped at 2–8°C

Long-term storage -20°C

Oxford Nanopore Technologies deem the useful life of the product to be 3 months from receipt by the customer.

Further considerations:

The direct RNA sequencing chemistry is new and both accuracy and throughput will continue to improve with future kit versions. 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 because they 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-RNA002) is used to prepare any RNA with a 3’ polyA tail for 1D sequencing on the Oxford Nanopore sequencing devices. Possible input RNA includes eukaryotic mRNA, viral RNA with a polyA tail, or any RNA prepared with a polyA-tailing kit. For RNA without a polyA tail, users can follow simple instructions to design their own custom adapter to ligate a specific terminal 3’ sequence like the 3’ of tRNA or 16S rRNA. The kit requires 500 ng of input RNA.

In contrast to cDNA sequencing protocols, which are used to prepare cDNA copies of RNA for sequencing, the Direct RNA kit is used to prepare RNA itself for sequencing. In Direct RNA sequencing, only the native RNA passes through the nanopore sensor thus the read length reflects the length of the RNA molecules in the sample.

The Direct RNA sequencing protocol contains an optional (but recommended) reverse transcription step and though the cDNA strand generated in this step is not sequenced, it significantly improves sequencing output.

2019 02 18 RNA002 v1 DS


Direct RNA sequencing - control experiment (SQK-RNA002)
Direct RNA sequencing (SQK-RNA002)
Direct RNA sequencing - sequence-specific (SQK-RNA002)

To access the protocols, you will need to register for a Nanopore Community account.

What's in the box

The Direct RNA Sequencing Kit contains sufficient reagents to generate six sequencing libraries

dRNA tubes

NameAcronymCap colourNo. of vialsFill volume per vial (μl)
RT AdapterRTABlue110
RNA Adapter MixRMXGreen145
RNA Calibrant StrandRCSYellow125
Wash BufferWSBOrange21,200
Elution BufferELBBlack1300
RNA Running BufferRRBRed1600

The Flow Cell Priming Kit is also supplied.


NameAcronymCap colourNo. of vialsFill volume per vial (μl)
Flush BufferFBBlue61,170
Flush TetherFLTPurple1200

3rd party materials


  • 1.5 ml Eppendorf DNA LoBind tubes
  • 0.2 ml thin-walled PCR tubes
  • Nuclease-free water (e.g. ThermoFisher, cat # AM9937)
  • Freshly prepared 70% ethanol in nuclease-free water
  • SuperScript III Reverse Transcriptase (Thermo Fisher Scientific, cat # 18080044)
  • 10 mM dNTP solution (e.g. NEB cat # N0447)
  • NEBNext® Quick Ligation Reaction Buffer (NEB B6058)
  • T4 DNA Ligase 2M U/ml (NEB M0202)
  • Agencourt RNAClean XP beads
  • Qubit RNA HS Assay Kit (ThermoFisher cat # Q32852)
  • Qubit dsDNA HS Assay Kit (ThermoFisher cat # Q32851)


  • Hula mixer (gentle rotator mixer)
  • Magnetic rack
  • Microfuge
  • Vortex mixer
  • Ice bucket with ice
  • Timer
  • Thermal cycler
  • P1000 pipette and tips
  • P100 pipette and tips
  • P20 pipette and tips
  • P10 pipette and tips
  • P2 pipette and tips

Optional equipment

  • Agilent Bioanalyzer (or equivalent)
  • Qubit fluorometer (or equivalent for QC check)
  • Eppendorf 5424 centrifuge (or equivalent)


The Direct RNA Sequencing Kit can be used together with:


  • Flow Cell Wash Kit (EXP-WSH004)

Flow cells

  • FLO-MIN106D
  • FLO-PRO002


  • MinION Mk1B
  • MinION Mk1C
  • GridION
  • PromethION