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KinnexFull-length RNA sequencing. Uncover the isoforms that drive biology.

Choose your kit

What Kinnex does

Up to 16-fold more throughput from every HiFi read

Kinnex increases the output of every HiFi read by 8-, 12-, or 16-fold for bulk RNA, 16S rRNA, single-cell RNA, and targeted amplicons.

Kinnex joins cDNA molecules or targeted amplicons into longer arrays for HiFi sequencing in order to increase sequencing throughput. Read segmentation then separates them into individual reads for analysis.

For RNA studies, those reads retain full-length transcript information. The preparation workflow and insert size determine which Kinnex kit to use.

What is an S-read? An S-read is a segmented read recovered from a Kinnex array. It can represent a cDNA molecule or a targeted amplicon. The table below reports S-reads for each kit.

From individual molecules to individual reads

1  cDNA molecules

Full-length cDNA or targeted amplicons.

2  Concatenated array

The kit joins molecules end to end, separated by segmentation adapters.

3  One HiFi read
HiFi consensus

Revio or Vega sequences the whole array as one HiFi read.

4  S-reads

Read segmentation separates the HiFi read at the adapters for downstream analysis.

Research in practice

Explore beyond gene-level expression

Rare disease · Blood and fibroblasts

Characterize splicing variants in rare disease

Jaramillo Oquendo, Ferraro, and colleagues ran Kinnex full-length RNA sequencing on blood and fibroblast samples from 25 people with suspected splice-altering variants, then compared the results against short-read RNA sequencing of the same participants.

Long reads confirmed 21 known splicing events and added transcript-level detail in eight cases, including intron retention, multiple exon skipping, leaky splicing, variant phasing, and isoform switching.

What this means for your study: Long-read RNA-seq improves identification and interpretation of clinically relevant splicing events in rare disease cohorts.

Jaramillo Oquendo et al., European Journal of Human Genetics, 2026. Peer-reviewed; includes PacBio co-authors. A study of an earlier workflow, not a benchmark for the SPRQ-Nx specifications below.

Read the study

Public datasets

See Kinnex data for yourself

Explore bulk RNA and single-cell data before planning your own analysis.

Bulk RNA datasets Human reference RNA and tissue samples Single-cell RNA datasets Human PBMC and HG002 samples

Check each dataset’s chemistry, library preparation, and system before making performance comparisons.

Choose your kit

Match the kit to your insert size

Start with your application and the peak or average insert size of your prepared library. Bulk RNA is compatible with 8-fold or 12-fold kits. Note: the ranges overlap, so size alone may not settle the choice.

16-fold prep kit under 1 kb 12-fold prep kit 1–2 kb 8-fold prep kit 1.5–3 kb OVERLAP 0 1 kb 1.5 kb 2 kb 3 kb
16-fold
Under 1 kb
103-836-900

For single-cell libraries and targeted amplicons with a peak or average insert size under 1 kb.

  • Single cell, and targeted amplicons
  • 100 – 150 M S-reads per Revio SMRT Cell (1 acquisition)
12-fold
1 – 2 kb
103-072-100

For bulk RNA, 16S rRNA, and targeted amplicons with a peak or average insert size of 1 – 2 kb.

  • Bulk RNA, 16S rRNA, and targeted amplicons
  • 70 – 100 M S-reads per Revio SMRT Cell (1 acquisition)
8-fold
1.5 – 3 kb
103-072-000

For bulk RNA, 16S rRNA, and targeted amplicons with a peak or average insert size of 1.5 – 3 kb.

  • Bulk RNA, 16S rRNA, and targeted amplicons
  • 50 – 70 M S-reads per Revio SMRT Cell (1 acquisition)
In the 1.5 – 2 kb overlap? Both 8-fold and 12-fold fall within the stated range. Review your application, library preparation, and read-depth needs with a scientist before selecting a kit. Get kit-selection help

Specifications

SPRQ-Nx chemistry

SPRQ-Nx chemistry on the Revio and Vega systems helps you get more out of every run. See S-read output by kit and system below.

On small screens, scroll the table horizontally to compare kits.

  Kinnex 8-fold prep kit Kinnex 12-fold prep kit Kinnex 16-fold prep kit
Part number 103-072-000103-072-100103-836-900
Applications Bulk RNA · 16S rRNA · Targeted amplicons Bulk RNA · 16S rRNA · Targeted amplicons Single-cell · Targeted amplicons
Peak insert size1 1.5 – 3 kb1 – 2 kbUnder 1 kb
S-reads
Revio SMRT Cell
(1 acquisition)		 50 – 70 M70 – 100 M100 – 150 M
Revio SMRT Cell-Nx
(3 acquisitions)		 150 – 210 M210 – 300 M300 – 450 M
Vega SMRT Cell
(1 acquisition)		 40 – 50 M50 – 60 M80 – 100 M

1 Peak or average size distribution of DNA inserts.
kb = kilobases · S-reads = segmented reads · M = million.

Plan your Kinnex experiment

Tell us your application, sample count, and insert size. A scientist can help you choose a kit and review your workflow.

Talk to a scientist View kits and ordering

Plan your workflow

From sample to isoform analysis

Match your library to your application and kit. Then choose the analysis workflow for your RNA data.

04

Call isoforms across many samples

Isocall joint-calls known and novel transcripts across many Iso-Seq samples at once, starting from reference-aligned FLNC reads. Isocall is a pre-release tool for research use and is in active development.

Isocall on GitHub Read the Isocall preprint

Already using Kinnex?

Check your kit before your next order

Products are now named 8-fold, 12-fold, and 16-fold. Confirm your part number, insert size, and application protocol when planning your next library.

Moving from the single-cell RNA kit

The Kinnex single-cell RNA kit (103-072-200) is being discontinued. Its replacement is the Kinnex 16-fold prep kit (103-836-900).

Review the replacement kit’s protocol and analysis requirements before switching.

Discuss your transition
Choosing a kit for bulk RNA or 16S

Both applications appear under 8-fold and 12-fold. Check the prepared library’s insert-size distribution and the application protocol. The old application name alone is not enough to choose a kit.

Compare the kit ranges

Questions

Kinnex FAQs

A few details to help you plan your experiment.

What is an S-read?

An S-read is a segmented read recovered from a Kinnex array. It can represent a cDNA molecule or a targeted amplicon.

How do I choose between 8-fold and 12-fold?

Use the peak or average insert size: 1.5–3 kb for 8-fold, and 1–2 kb for 12-fold. When size overlaps (e.g. 1.5 kb), choose between higher average read level quality (8-fold), or throughput (12-fold).

Where can I find preparation and analysis requirements?

Use PacBio documentation to find the preparation protocol for your application and kit. For command-line analysis, follow the bulk RNA guide or single-cell RNA guide. Confirm that the instructions apply to your kit and software version.

Is there an option to increase cDNA barcodes beyond the 12 provided in the Iso-Seq kit?

Yes. PacBio publishes an additional set of 96 5′ single-end cDNA primers for use with the Iso-Seq Express 3p cDNA amplification primer. There is no overlap with the Iso-Seq Express 2.0 set. Order them from your preferred oligo vendor. The published FASTA file is on the Multiplexing webpage: download the 96-primer set.

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.