NEXTflex™ Small RNA Sequencing Kit v3 for Illumina® Platforms

Gel-free or low input small RNA library prep kit with reduced bias for Illumina® sequencing

Catalog# Product Name Quantity US List Price
5132-05 NEXTflex™ Small RNA-Seq Kit v3 (8 barcodes)
8 rxns $525 Buy Now
5132-06 NEXTflex™ Small RNA-Seq Kit v3 (48 barcodes) 48 rxns $2,626 Buy Now

NEXTflex™ Small RNA-Seq Kit v3
  • Completely gel-free protocol with normal input amounts
  • Greater discovery/detection rates reduces sequencing cost
  • Randomized adapters reduce ligation bias, resulting in more accurate data
  • Low input (1 ng) gel-based protocol included
  • AIR™ Ligase offers greater sequencing depth
  • Use more of your RNA sample - 10.5 µL input volume
  • Barcoded primers are included in the kit allowing multiplexing of up to 48 samples
  • An automation protocol is available for the PerkinElmer® Sciclone® NGS and NGSx Workstation
  • Functionally validated with Illumina® sequencing platforms

For Research Use Only. Not for use in diagnostic procedures.

Gel-Free Small RNA Library Prep with Randomized Adapters for Reduced Bias

The NEXTflex™ Small RNA-Seq Kit v3 uses patented and patent-pending technology to provide a reduced-bias small RNA library preparation solution for Illumina® sequencing platforms with gel-free or low-input options. Bioo Scientific’s approach to reducing ligation-associated bias involves the use of adapters with randomized bases at the ligation junctions, resulting in greatly decreased bias in comparison to standard protocols. This reduction in bias results in data that more accurately represents abundances of small RNAs in the starting material. In addition, reduction of bias allows more miRNAs to be detected with fewer total reads, increasing efficiency and reducing cost for small RNA sequencing. 

PAGE purification, required for traditional small RNA library prep, is tedious, time consuming, limits throughput, and prevents start-to-finish automation. The NEXTflex Small RNA-Seq Kit v3 allows for gel-free small RNA library preparation. This is possible thanks to the dual approach used for adapter-dimer reduction. Unprecedented reduction of adapter-dimer formation allows completely gel-free small RNA library prep when starting with ≥200 ng of total RNA. Libraries prepared with the NEXTflex Small RNA-Seq kit v3 have a higher proportion of reads mapping to miRNAs (Fig. 1).

Gel-free libraries prepared with the NEXTflex Small RNA-Seq kit v3 have a higher proportion of reads mapping to miRNAs

Figure 1. Small RNA libraries were created in duplicate from the human brain total RNA and sequenced on an Illumina MiSeq. The indicated number of reads were sampled from each library and the average number of miRNA groups with ≥20 reads determined. The inset shows the number of reads required to detect 100 miRNA groups at a threshold of ≥20 reads.

Low Input Small RNA Library Prep for Illumina® Sequencing

The adapter-dimer reduction technology incorporated into this kit also allows low input library preparation. Library preparation with as little as 1 ng of total RNA is possible as additional PCR cycles can be performed without adapter-dimer products dominating the final library. Fig. 2 illustrated that expression values are reproducible across different sample inputs.

Correlation of miRNA expression between samples created with 100 ng and 10 ng of human brain total RNA with the NEXTflex Small RNA-Seq kit v3

Figure 2. Correlation of miRNA expression between samples created with 100 ng and 10 ng total RNA from human brain with the NEXTflex Small RNA-Seq kit v3. The Pearson correlation coefficient is shown. 

Illumina Small RNA-Seq Multiplexing

Eight barcoded primers are included in the eight reaction NEXTflex Small RNA-Seq Kit v3 and forty-eight barcoded primers are included in the forty-eight reaction NEXTflex Small RNA-Seq Kit v3.

Small RNA-Seq Automation Compatibility

The NEXTflex Small RNA-Seq Kit V3 was designed for easy migration onto automated liquid handling platforms. Currently methods are available for the PerkinElmer® Sciclone® NGS and NGSx Workstation.

Download the Sciclone® NGS and NGSx Workstation Automation Guide for the NEXTflex Small RNA-Seq Kit V3.

For more information contact

Selected Citations that Reference the Use of the NEXTflex Small RNA-Seq Kit V3

Palanichamy, J. K., et al. (2016) RNA-binding protein IGF2BP3 targeting of oncogenic transcripts promotes hematopoietic progenitor proliferation. J Clin Invest. doi:10.1172/JCI80046.


In our studies, we found that NEXTflex v2 is able to detect robustly several functionally important miRNAs that partially or completely evade detection by the widely used Illumina library preparation protocols

Kit Specs

The NEXTflex Small RNA Sequencing Kit v3 contains the reagents, including barcoded primers, to prepare 8 or 48 small RNA samples for Illumina® next-generation sequencing. The shelf life of all reagents is 6 months when stored properly at -20°C. Ships on dry ice.

NEXTflex™ Small RNA-Seq Library Prep Kit v3 Protocol for Illumina® Small Library Prep

NEXTflex Illumina Small RNA Library Prep Kit v3 Flowchart


Kit Contents

NEXTflex™ 3’ 4N Adenylated Adapter
NEXTflex™ 3’ Ligation Buffer
NEXTflex™ 3’ Ligation Enzyme Mix
NEXTflex™ Adapter Depletion Solution
NEXTflex™ Adapter Inactivation Buffer
NEXTflex™ Adapter Inactivation Enzyme
NEXTflex™ 5’ 4N Adapter
NEXTflex™ 5’ Ligation Buffer
NEXTflex™ 5’ Ligation Enzyme Mix
M-MuLV Reverse Transcriptase
NEXTflex™ RT Buffer
NEXTflex™ Universal Primer
NEXTflex™ Barcode Primer
NEXTflex™ Small RNA PCR Master Mix
6X Loading Dye
Ready to Load Low MW Ladder
Resuspension Buffer
Nuclease-free Water
microRNA Control
NEXTflex™ Cleanup Beads
NEXTflex™ Elution Buffer


Required Materials Not Provided

1 ng - 2 μg total RNA or purified small RNA from 1-10 μg total RNA in up to 10.5 μL Nuclease-free Water
80% Ethanol
2, 10, 20, 200 and 1000 μL pipettes
RNase-free pipette tips
96 well PCR Plate Non-skirted (Phenix Research®, Cat # MPS-499) or similar
Thin-wall nuclease-free PCR tubes
Heat block
Magnetic Stand -96 (Thermo Fisher Scientific®, Cat # AM10027) or similar

Using the NEXTflex Small RNA-Seq Kit v3 for alternative RNA inputs, including  RIP-Seq, CLIP-Seq, HITS-CLIP, and Ribosomal Profiling

Although NEXTflex Small RNA Sequencing Kits are normally used to prepare sequencing libraries representing miRNAs, siRNAs, or piRNAs, the kits can also be used to create libraries from other RNA samples, such as RNA isolated from ribosomal profiling, RIP-Seq (RNA binding protein immunoprecipitation and sequencing), CLIP-Seq (cross-linking immunoprecipitation and sequencing), and HITS-CLIP experiments. To create sequencing libraries with NEXTflex Small RNA Sequencing Kits, the RNA of interest should have a 5' monophosphate and 3' hydroxyl. Fortunately, these modifications can easily be added to most RNA molecules with T4 polynucleotide kinase (PNK). PNK contains both 5' kinase and 3' phosphatase activities, making it ideal for preparing RNA samples for library preparation with the NEXTflex™ Small RNA Seq Kit v3.

In order to prepare a library from RNA molecules that do not already contain a 5' monophosphate and 3' hydroxyl, the following basic strategy can be followed:

1. Treat RNA with T4 PNK according to the manufacturer's instructions. A 10 minute pre-incubation with all components except ATP may help increase the phosphatase activity, which will lead to greater yield for RNA samples that contain 3' phosphates, such as those that have undergone chemical/heat fragmentation.

2. Purify RNA using ethanol precipitation or a column-based kit, such as the Zymo RNA Clean and Concentrator-5. Resuspend/elute the RNA in ~12 µL of water.

3. Optional Check RNA size and approximate quantity by Agilent Bioanalyzer. Note that Bioanalyzer estimates of concentration are often inaccurate, so this value should be treated as an estimate.

4. Prepare libraries using the NEXTflex Small RNA-Seq Kit v3. If ≥ 1 ng of PNK-treated RNA is used for library prep, 15 cycles or fewer of PCR should be sufficient.

The default protocol enriches for final library products representing RNA molecules of ~20-30 nt. In order to retain products representing larger RNA fragments, the protocol should be modified according to the instructions in the NEXTflex Small RNA Seq Kit v3 No Size Selection Supplement.

5. If a final size selection is desired, gel-based size selection can be performed, or the volumes used in Step H1: Gel-Free Size Selection & Cleanup can be optimized for the desired size range (contact us at for recommendations). Note that bead-based methods only achieve coarse size selection, so PAGE purification is recommended if precise size selection is needed. 

Can the Sage® Pippin Prep® system be used for automated size selection of small RNA libraries created with the NEXTflex™ Small RNA Sequencing Kit v3?

Yes, a protocol is available for automated size selection of small RNA libraries constructed using the NEXTflex™ Small RNA Sequencing Kit v3. Download the Sage® Pippin Prep® protocol for the NEXTflex Small RNA-Seq Kit v3.

What is the lowest input of total RNA possible with this kit?

The lowest recommended input is 1 ng of total RNA. This amount of RNA should work well for most sample types. For samples that have high miRNA content, less total RNA may be used.

Why do I have to perform a cleanup after 3' ligation? This step is not necessary in other kits.

Typical "tricks" to reduce formation of adapter-dimer do not work well when using adapters with randomized ends, which is the reason for the Excess 3' Adapter Depletion step.

Is this kit compatible with both single read and paired-end sequencing?

Yes, in addition to single read sequencing this kit can also be used with paired-end sequencing.

Will the random nucleotides from the adapters be present in my sequencing reads?

Yes, the random bases will be present as the first four bases of the read and the four bases immediately before the 3' adapter sequence.

How should the random bases be handled for alignment?

Following 3' adapter trimming, the first and last four bases of the read should be trimmed prior to alignment. Another option is to use an aligner with a "local" mode.

What sequencing platforms is this kit compatible with?

This kit is compatible with all common Illumina® sequencing platforms including the HiSeq®, MiSeq®, and NextSeq® 500 systems.

How many sequencing cycles do small RNA libraries need?

This is dependent on your experiment and whether you’re looking at microRNAs or long non-coding RNAs. For microRNAs, we do not recommend fewer than 36 sequencing cycles. The Illumina® MiSeq® 1x50 cycle run is most commonly used for sequencing microRNAs. Most microRNAs are between 15–30 bases long, and sequencing beyond this point only sequences the adapter.

How many reads are needed per sample for small RNA sequencing?

This is also dependent on your experiment. Generally for expression profiling, 1–2M mapped reads is an accepted range. For discovery applications, you may want to increase to 2–5M reads.  Contact us at and we can help you determine the best number of reads based on your experimental design.

How are the barcoded primers incorporated into the small RNA-Seq libraries?

The NEXTflex™ Small RNA Barcodes Primers, each containing a six-base index, are incorporated into the library during the PCR amplification step. This design allows for the indexes to be read using a second read, which reduces bias.

During size selection on 6% PAGE gel, which bands should I cut out of the gel?

MicroRNAs that are between 20 – 30 nt in length will yield a band ~150 -160 bp in length, which should be cut out of the 6% PAGE gel. Do not cut out the ~130 bp band as this is adapter dimer.

What is AIR™ Ligase and why is it used in the NEXTflex Small RNA-Seq Kit v3?

AIR Ligase is an enhanced, truncated T4 RNA Ligase, which increases the efficiency with which small RNAs are tagged with adapter, giving greater sequence depth.

This kit recommends up to 25 cycles of PCR amplification for low-input libraries. Won’t this many PCR cycles intro bias?

No, PCR has been shown to introduce negligible bias into small RNA libraries. See publications by Jayaprakash, et al., Hafner, et al. and our whitepaper for more information.

Jayaprakash, A.D., et al., Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing. Nucleic Acids Res, 2011. 39(21): p. e141.

Hafner, M., et al., RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA, 2011. 17(9): p. 1697-712.