What is Kinnex?
The Kinnex kits are based on the MAS-Seq method, which concatenates smaller amplicons into larger fragment libraries for throughput increase.
Kinnex kits increase throughput for full-length RNA, single-cell RNA, and 16S rRNA sequencing on PacBio long-read sequencing systems to enable large-scale studies at a resolution difficult to attain with short-read RNA sequencing.
Want to watch more Kinnex webinars? Learn from tutorials? See how it’s being used by other researchers? Check out the Kinnex YouTube playlist.
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Kinnex for Human Genomics Research
HiFi on the brain – advancing Parkinson’s disease research using HiFi sequencing
In this webinar, learn about the sequencing technology that is pushing neuroscience research forward, particularly in Parkinson’s disease. Discover how HiFi whole genome sequencing (WGS) and the PacBio Iso-Seq method provide complete visibility into all genomic variants, reveal crucial transcript isoform information, and ultimately enable the potential development of novel therapeutics.
Detecting shared mis-splicing across blood cancers using long-read single-cell RNA sequencing
In this webinar, discover how long-read single-cell RNA sequencing with the PacBio Kinnex single-cell RNA kit successfully validated shared mis-splicing patterns in adult and pediatric AML. See how innovative computational approaches helped identify dominant splicing subtypes that drive disease progression, providing insight into underlying mechanisms and revealing isoform-level differences linked to disease prognosis.
Characterizing C9orf72 repeat expansions and transcripts using HiFi sequencing
In this webinar hear from Mayo Clinic scientist, Evan Udine, on using the PureTarget and Kinnex kits, alongside other PacBio technologies, to push the boundaries of neurodegenerative disease research. The PureTarget repeat expansion panel offers comprehensive sequence information for pathogenic repeats, providing clarity where short reads and traditional methods may fall short, while the Kinnex full-length RNA kit complements genome sequencing by detailing the transcriptome complexities of neurodegenerative diseases.
Webinar video
Automating Kinnex kits with SPT Labtech firefly system
Hear how the Seattle Children’s Research Institute uses the SPL Labtech firefly liquie handler to automate Iso-Seq cDNA synthesis and Kinnex full-length RNA library construction to support the 1000 Genomes Long Read Project.
Isoform quantification using deep coverage long-read RNA-Seq
Researchers at ETH Zurich and UVA applied Kinnex full-length RNA-Seq to deeply sequence WTC-11 cell line over multiple timepoints and replicates to create the largest single cell line long-read RNA-Seq dataset to date. They showed Kinnex demonstrates better and consistent isoform detection and quantifiability compared to short reads, especially in cases of complex alternative splicing.
Read the pre-print Watch the webinar Read the blog
Kinnex FAQs
Kinnex is a library method for concatenating amplicons for higher throughput on PacBio long-read sequencing systems. It is based on the MAS-Seq method developed by Al’Khafaji et al. (2023).
The three Kinnex kits are tailored for three different amplicon sizes and applications. The Kinnex full-length RNA kit is suited for bulk transcriptome sequencing, the Kinnex 16S rRNA kit is suited for full-length 16S rRNA, and the Kinnex single-cell RNA kit is suited for single-cell cDNA generated by compatible platforms including 10x Genomics single-cell cDNA and Parse Biosciences. However, Kinnex kits also work as general amplicon concatenation kits and can be modified to work with a variety of amplicons.
Kinnex kits are compatible with PacBio long-read systems including Sequel II/IIe, Vega, and Revio systems.
Kinnex full-length RNA kit: ~20M on Sequel II/IIe systems, ~30M on Vega system, and 60M on Revio with SPRQ chemistry.
Kinnex 16S rRNA kit: ~25M on Sequel II/IIe systems, ~40M on Vega system, and ~80M on Revio with SPRQ chemistry.
Kinnex single-cell RNA kit: ~40M on Sequel II/IIe systems, ~60M on Vega system, and ~120M on Revio with SPRQ chemistry.
Yes, Kinnex kits support 10x Chromium Universal 3’ kit (v3.1, v4) and Universal 5’ kit (v2, v3).
Different amplicons support different levels of multiplexing. The Iso-Seq express 2.0 kit supports 12-plex for bulk cDNA synthesis. The Kinnex 16S rRNA protocol provides primer design supporting up to 384-plex at the amplicon level. Additionally, Kinnex kits use the same set of four barcoded adapters.
Yes. The Iso-Seq express 2.0 kit and Kinnex full-length RNA kits have been automated and tested on the SPT Labtech firefly system. The Kinnex PCR portion for all three Kinnex kits are also automated on the Opentrons OT-2 system.
SMRT Link provides both GUI and command line-based analysis workflow for bulk transcriptome (Read Segmentation & Iso-Seq workflow), single-cell transcriptome (Read Segmentation & Single-cell Iso-Seq workflow), and general de-concatenation of the amplicons for other Kinnex applications (Read Segmentation). Additional Bioconda-based command line tutorials can be found at: https://isoseq.how/
You can visit Kinnex youtube playlist to watch webinars and tutorials!
Whitepaper
Full-length bulk and single-cell RNA sequencing for cancer research
The Iso-Seq method (full-length RNA sequencing using PacBio HiFi sequencing) has been shown to advance cancer research by unambiguously characterizing isoforms at both the bulk and single-cell level. PacBio Kinnex RNA kits further increase throughput on HiFi long-read sequencers. This whitepaper highlights publications on cancer research to demonstrate how bulk and single-cell Iso-Seq data detects fusion genes, identifies novel isoforms that might serve as neoepitopes for vaccine candidates, and traces clonal evolution.
Kinnex application kits
 |  |  | ||||
| Kinnex full-length RNA kit | Kinnex single-cell RNA kit | Kinnex 16S rRNA kit | ||||
| Kit advantage | Full-length isoform discovery with flexible sample multiplexing | Cell type-specific isoform isoform discovery with the highest accuracy | Full-length 16S rRNA for species identification | |||
| Total throughput | 15-20M (Sequel II) | 30-40M (Sequel II) | 20-25M (Sequel II) | |||
| Sample multiplexing recommendation* | 5M × 3-plex (Sequel II) | 1-plex (Sequel II) | 384-plex (Sequel II) | |||
| Analysis | SMRT Link v13.0 and above | SMRT Link v13.1 and above | SMRT Link v13.0 and above | |||
| Read the tertiary tools app note | Read the tertiary analysis wiki | |||||
| * Sample multiplexing and read depth recommendation will vary by experimental goal, tissue, and species. | ||||||
Technical note
Concatenating cDNA or gDNA amplicons using Kinnex kits to increase throughput
Kinnex kits can be used as a general concatenation kit for cDNA or gDNA amplicons, which can increase the throughput by 8-, 12-, or 16-fold, and decrease sequencing cost. Read the tech note to see how you can use or modify your amplicon for cost-effective sequencing with Kinnex kits on PacBio’s long read sequencers.
“Long-read RNA sequencing results in more accurate measurements than any obtained from short-read RNA-Seq to determine the presence or absence of specific isoforms.”
Schertzer et al. (2024)
Targeted enrichment for Kinnex full-length RNA kit using IDT xGen HybWash v3 Reagents
The IDT xGen Hybridization and Wash kit v3 (early access) is compatible with the Kinnex full-length RNA kit. Enrich for rare isoforms of target genes and increase sample multiplexing with targeted enrichment.
Read protocol View dataset Read tech note
On-demand webinar
Leveraging isoform-level RNA sequencing to understand rare disease pathogenesis
See how researchers compared their experience analyzing Kinnex full-length RNA data against other sequencing technologies. Cleaner data – faster path to biological insight
RNA sequencing datasets
FEATURED LONG-READ SEQUENCING SYSTEMS
Achieve highly accurate full-length cDNA sequencing with PacBio long-read sequencers.