Resources: Documentation

Extraction of ultra-high molecular weight (uHMW) gDNA - Reliably generate and sequence ultra-long read length N50s (>50 kb) - High yield - Compatible with R10.4.1 flow cells For Research Use Only __This is an Early Access product__ __For more information about our Early Access programmes, please see [this article on product release phases](https://nanoporetech.com/about-us/news/blog-you-cant-put-label-innovation-or-can-you).__

For Research Use Only This is a registration-based Early Access product.

10X Genomics Visium Spatial transcriptomics method: - Requires cDNA amplicons produced using the Visium Spatial Gene Expression assay (Visium V1 for Fresh Frozen) or the Visium HD 3' Spatial Gene Expression assay - Library preparation time ~205 minutes - High output - PCR required For Research Use Only

Single-cell transcriptomics method: - Requires cDNA amplicons produced using the 10x Genomics Chromium GEM-X Universal 3’ Gene Expression (V4) assay or the Chromium Next GEM Universal 3’ Gene Expression (V3.1) assay. - Library preparation time ~205 minutes - High output - PCR required For Research Use Only

For Research Use Only

The effect of varying the number of PCR cycles in the PCR-cDNA Sequencing Kit

Telomere-to-telomere sequencing (T2T) know-how document

Stability of SPRI size selection beads

Short Fragment Eliminator Kit (EXP-SFE001) know-how document

Direct-from-colony microbial sequencing: rapid Salmonella serotyping know-how and info sheet

RNA stability

RNA Integrity Number (RIN)

Rapid metagenomic sequencing for surveillance of bacterial, fungal and viral pathogens using SQK-RPB114.24 know-how document

Polyadenylation of non-poly(A) transcripts using E. coli poly(A) polymerase

Accurate poly(A) tail length estimation for Direct RNA Sequencing (SQK-RNA002) and cDNA (SQK-PCS111, SQK-PCB111.24) sequencing kits

Ligation Sequencing sample input and flow cell loading know-how

DNA library stability - Ligation Sequencing Kit

Flow Cell Wash Kit (EXP-WSH004 or EXP-WSH004-XL) know-how

Enrichment of polyadenylated RNA molecules know-how document

DNA stability - storage

DNA stability - freeze-thawing

Chromatin accessibility know-how document

Updated method for cell-free DNA (cfDNA) methylation profiling

Optimisation of library preparation for longer cell-free DNA (cfDNA) libraries

Assessment of cfDNA extraction kits for nanopore sequencing

Comparative analysis of cfDNA collection tubes for nanopore sequencing

Cell storage

Blood storage

Telo-Seq know-how document

A method to remove amplified cDNA artefact in SQK-PCS111 and SQK-PCB111.24 libraries

Sequencing products of multiple displacement amplification (MDA)

A method to remove highly abundant globin transcripts from human blood RNA samples

Adeno-associated virus (AAV) sequencing - development notes and best practices

For Research Use Only.

The fastest and simplest protocol to sequence plasmid DNA - For multiplexing up to 96 samples - Library preparation time ~60 minutes - High yield - Fragmentation - Compatible with R10.4.1 flow cells For Research Use Only

The fastest and simplest protocol to sequence amplicon DNA - For multiplexing up to 96 single species amplicon samples - Optimised for 500 bp – 5 kb amplicons. - Library preparation time ~60 minutes - High yield - Fragmentation - Compatible with R10.4.1 flow cells For Research Use Only

The fastest and simplest protocol for genomic DNA involving: - ~10 mins library prep - Fragmentation - No third-party ligase needed - No PCR __This is an Early Access product__ __For more information about our Early Access programmes, please see [this article on product release phases](https://nanoporetech.com/about-us/news/blog-you-cant-put-label-innovation-or-can-you).__ For Research Use Only

This protocol: - is a rapid method to perform metagenomic sequencing for identification of bacterial, fungal and viral pathogens. - consists of a two-in-one method that splits sample into bacterial/fungal sample preparation and viral/acellular sample preparation. - provides a recommended host depletion and extraction method for respiratory samples. - uses a shotgun approach to RT-PCR. - involves tagmentation, barcoding and PCR amplification. - is compatible with R10.4.1 flow cells. <br> For Research Use Only __This is an Early Access product__ __For more information about our Early Access programmes, please see [this article on product release phases](https://nanoporetech.com/about-us/news/blog-you-cant-put-label-innovation-or-can-you).__

This protocol uses genomic DNA - For multiplexing 1-96 samples - Library preparation time ~60 minutes - High yield - Fragmentation - Compatible with R10.4.1 flow cells For Research Use Only

This protocol: - uses genomic DNA - has a low input requirement - method involves tagmentation, barcoding and PCR amplification - allows multiplexing of 1–24 samples - is compatible with R10.4.1 flow cells <br> For Research Use Only __This is an Early Access product__ __For more information about our Early Access programmes, please see [this article on product release phases](https://nanoporetech.com/about-us/news/blog-you-cant-put-label-innovation-or-can-you).__

A protocol for amplifying the 16S rRNA gene from extracted gDNA. - Genus-level bacterial identification - Multiplex up to 24 different samples - Compatible with R10.4.1 flow cells only For Research Use Only

The fastest and simplest protocol for genomic DNA involving: - ~10 mins library prep - fragmentation - no third-party ligase needed __This is an Early Access product__ __For more information about our Early Access programmes, please see [this article on product release phases](https://nanoporetech.com/about-us/news/blog-you-cant-put-label-innovation-or-can-you).__ For Research Use Only

Automated rapid barcoding method using the ElysION device outlining library preparation and sequencing. This protocol: * Is an automated method using the ElysION device * Uses genomic DNA * Enables multiplexing of up to 96 samples * Includes DNA fragmentation * Is optimised for high output * Is compatible with R10.4.1 flow cells <br> __For Research Use Only__ This method is user with an Early Access device. For more information about our Early Access programmes, please refer to this article on [product release phases](https://nanoporetech.com/news/news-blog-you-cant-put-label-innovation-or-can-you).

This protocol provides an end-to-end workflow for the analysis of pharmacogenomic (PGx) genes using adaptive sampling, and the Oxford Nanopore platform. Downstream variant calling is via the EPI2ME™ wf-pgx workflow, acquiring a minimum of 40x coverage per sample, across the PGx-associated genes. The protocol covers genomic DNA extraction, mechanical shearing, native barcoding, library preparation, sequencing, and data analysis. It supports the multiplexing of up to four samples per PromethION™ Flow Cell and is compatible with DNA extracted from human whole blood, cultured cells, or saliva. This protocol: - Uses genomic DNA extracted from human whole blood, cultured cells, or saliva - Requires DNA fragmentation - Uses the Native Barcoding Kit 24 V14 (SQK-NBD114.24) - Is compatible with R10.4.1 flow cells - Allows the analysis of data using the wf-pgx workflow in EPI2ME <br> **For Research use only**

This protocol uses extracted RNA samples - Includes reverse transcription and tiled PCR amplification - For multiplexing 1-96 samples - Library preparation time ~315 minutes - Fragmentation - Compatible with R10.4.1 flow cells For Research Use Only __This is an Early Access product__ __For more information about our Early Access programmes, please see [this article on product release phases](https://nanoporetech.com/about-us/news/blog-you-cant-put-label-innovation-or-can-you).__

The fastest and simplest protocol for full-length cDNA sequencing - Offering highest yield - Higher yields than traditional cDNA synthesis - Splice variants and fusion transcripts - Compatible with R10.4.1 flow cells <br> For Research Use Only __This is an Early Access product__ __For more information about our Early Access programmes, please see [this article on product release phases](https://nanoporetech.com/about-us/news/blog-you-cant-put-label-innovation-or-can-you).__

The fastest and simplest protocol for full-length cDNA sequencing - Offering highest yield - Higher yields than traditional cDNA synthesis - Splice variants and fusion transcripts - Multiplex up to 24 different samples - Compatible with R10.4.1 flow cells only <br> For Research Use Only __This is an Early Access product__ __For more information about our Early Access programmes, please see [this article on product release phases](https://nanoporetech.com/about-us/news/blog-you-cant-put-label-innovation-or-can-you).__

End-to-end method outlining sample extraction, library preparation, sequencing and data analysis. This protocol: * Uses genomic DNA * Enables multiplexing of 4-24 samples * Takes ~60 minutes for library preparation * Includes DNA fragmentation * Is optimised for high output * Is compatible with R10.4.1 flow cells <br> __For Research Use Only__

Automated native barcoding method using the ElysION device outlining library preparation and sequencing. This protocol: * Is an automated method using the ElysION device * Enables multiplexing of up to 48 samples * Allows analysis of native DNA * Is a PCR-free method * Is compatible with R10.4.1 flow cells <br> __For Research Use Only__ This method is used with an Early Access device. For more information about our Early Access programmes, please refer to this article on [product release phases](https://nanoporetech.com/news/news-blog-you-cant-put-label-innovation-or-can-you).

This protocol uses genomic DNA - Hands-on setup time ~30 minutes - Automated run time ~3 hours 40 minutes - Throughput: Process 6–96 samples for multiplex library loading - Compatible with R10.4.1 Flow Cells For Research Use Only

Single-cell transcriptomics method: - Requires cDNA amplicons produced using the 10x Genomics Chromium GEM-X Universal 5' Gene Expression (V3) assay or the Chromium Next GEM Universal 5' Gene Expression (V2) assay - Library preparation time ~135 minutes - High output - PCR required For Research Use Only

Method outlining sample extraction, library preparation, sequencing and data analysis. This protocol: * uses human cfDNA * is for singleplex sequencing * is compatible with R10.4.1 flow cells <br> __For Research Use Only__

Method outlining sample extraction, library preparation, sequencing and data analysis. This protocol: * uses human cfDNA * enables multiplexing of 12 samples * is compatible with R10.4.1 flow cells <br> __For Research Use Only__

The PCR-free protocol for full-length cDNA offers: - Higher yields than traditional cDNA synthesis - Analysis of splice variants & fusion transcripts - Compatibility with R10.4.1 flow cells For Research Use Only

This protocol uses extracted RNA samples - Includes reverse transcription and PCR amplification using two separate primer schemes for Influenza A and Influenza B - Includes quantification and normalisation steps to ensure equal distribution of barcodes for 24, 48 and 96 samples. - Compatible with R10.4.1 flow cells <br> For Research Use Only

- This protocol uses genomic DNA - Has very low input requirements (e.g. single cells) - Uses multiple displacement amplification (MDA) - Is compatible with R10.4.1 flow cells For Research Use Only

End-to-end method outlining sample extraction, library preparation, sequencing and data analysis. This protocol: - Uses genomic DNA extracted from human blood samples - Takes ~300 minutes for sample preparation and ~90 minutes for library preparation. - Requires no PCR - Is compatible with R10.4.1 flow cells __For Research Use Only__

Sequencing of adeno-associated virus (AAV) vectors. * Requires the Native Barcoding Kit 24 V14 (SQK-NBD114.24) * Includes no PCR steps * Uses up to 24 barcodes * Allows analysis of native DNA * Compatible with R10.4.1 flow cells For Research Use Only

This protocol uses N50 of 30 kb genomic DNA extracted from human cell lines * Sample preparation time: ~320 minutes and library preparation time: ~90 minutes * Data analysis: 1-2 hours * No PCR * Compatible with R10.4.1 flow cells For Research Use Only

This protocol uses N50 of 10 kb genomic DNA extracted from human cell lines - Sample preparation time: ~220 minutes and library preparation time: ~90 minutes - Data analysis: 1-2 hours - No PCR - Compatible with R10.4.1 flow cells For Research Use Only

This protocol uses genomic DNA - Library preparation time ~65 minutes - Fragmentation optional - No PCR required - Suitable for processing multiple samples simultaneously, or automated library preparation - Compatible with R10.4.1 flow cells For Research Use Only

This protocol: - Requires the PCR Barcoding Expansion (EXP-PBC001 or EXP-PBC096) with the Ligation Sequencing Kit V14 (SQK-LSK114) - Barcodes gDNA or amplicons - Has a library preparation time ~155 minutes + PCR - Results in high yield - Uses up to 96 barcodes - Includes PCR steps - Is compatible with R10.4.1 flow cells For Research Use Only

Barcoding of native genomic DNA libraries - Requires the Native Barcoding Kit 96 V14 (SQK-NBD114.96) - PCR-free protocol - Using up to 96 barcodes - Allows analysis of native DNA - Compatible with R10.4.1 flow cells For Research Use Only

Barcoding of native genomic DNA libraries - Requires the Native Barcoding Kit 24 V14 (SQK-NBD114.24) - PCR-free protocol - Using up to 24 barcodes - Allows analysis of native DNA - Compatible with R10.4.1 flow cells For Research Use Only

For barcoding of native genomic DNA libraries - Requires the Multiplex Ligation Sequencing Kit V14 XL - No PCR required - Features 96 unique barcodes - Enables low-plex sequencing - Allows analysis of native DNA - Compatible with R10.4.1 flow cells <br> For Research Use Only

For Research Use Only.

This protocol: - Requires the PCR Expansion (EXP-PCA001) with the Ligation Sequencing Kit V14 (SQK-LSK114) - Uses genomic DNA, amplicons or cDNA - Results in high yield - Has a library preparation time ~145 minutes + PCR - Includes PCR steps - Is compatible with R10.4.1 flow cells For Research Use Only

This protocol uses Lambda control DNA - Library preparation time ~65 minutes - Fragmentation optional - No PCR - Compatible with R10.4.1 flow cells For Research Use Only

For barcoding genomic or amplicon DNA for nanopore sequencing. - Offering highest accuracy - Multiplexing up to 2,304 samples - Requires PCR steps - Compatible with R10.4.1 flow cells <br> For Research Use Only

This protocol uses amplicon DNA - Library preparation time ~75 minutes - Fragmentation optional - No PCR For Research Use Only

Barcoding of amplicon libraries - Requires the Native Barcoding Kit 96 V14 (SQK-NBD114.96) - Includes no PCR steps - Using up to 96 barcodes - Allows analysis of native DNA - Compatible with R10.4.1 flow cells For Research Use Only

Barcoding of amplicon libraries - Requires the Native Barcoding Kit 24 V14 (SQK-NBD114.24) - Includes no PCR steps - Using up to 24 barcodes - Allows analysis of native DNA - Compatible with R10.4.1 flow cells For Research Use Only

This protocol is for recovering DNA libraries from flow cells for continued sequencing - Compatible with both MinION and PromethION flow cells, and all DNA sequencing kits For Research Use Only

For Research Use Only

End-to-end method outlining sample extraction, library preparation, sequencing and data analysis. This protocol: - Uses genomic DNA extracted from human saliva samples - Takes ~300 minutes for sample preparation and ~90 minutes for library preparation. - Requires no PCR - Is compatible with R10.4.1 flow cells __For Research Use Only__

End-to-end method outlining sample extraction, library preparation, sequencing and data analysis. This protocol: - Uses genomic DNA extracted from human buccal swab samples - Takes ~90 minutes for sample preparation and ~135 minutes for library preparation. - Requires no PCR - Is compatible with R10.4.1 flow cells __For Research Use Only__

This protocol uses genomic DNA - Library preparation time ~65 minutes - Fragmentation optional - No PCR - Compatible with R10.4.1 flow cells For Research Use Only

For Research Use Only

Yeast DNA

Yeast DNA (Community-developed)

Mycobacterium tuberculosis DNA

SPRI size selection protocol for >1.5-2 kb DNA fragments

Soil DNA

Removal of short fragments with the Short Fragment Eliminator Kit (EXP-SFE001)

Human blood cell-free DNA (cfDNA) extraction for singleplex sequencing

Human cell line RNA

Plasmid DNA extraction method

Fruit fly (Drosophila melanogaster) RNA

Button mushroom (Agaricus bisporus) DNA

Human blood cell-free DNA (cfDNA) extraction for multiplex sequencing

Reptile tissue DNA

Human saliva DNA

Alpha and beta globin mRNA depletion from total RNA extracted from human blood

Human blood RNA

High output, long read sequencing from human blood

Gram-negative bacterial DNA

Western clawed frog (Xenopus tropicalis) muscle DNA

Influenza A RNA

FFPE human cell DNA

Environmental water (eDNA)

Automated gDNA extraction from dry blood spots (FTA cards)

Fruit fly (Drosophila melanogaster) DNA

Whole genome colony PCR

Worm (Caenorhabditis elegans) RNA

Worm (Caenorhabditis elegans) DNA

Extracting and preparing DNA from brain tissue for Oxford Nanopore Sequencing

Arabidopsis (Arabidopsis thaliana LEr) leaf RNA

Agarose plug DNA

3’ polyadenylation of RNA transcripts using E. coli poly(A) polymerase (PAP)

Yeast cell culture RNA

Stool pellet gDNA

Size selection

Salmon sample gDNA

Rabbit skin gDNA

Rabbit muscle gDNA

Rabbit lung gDNA

Rabbit fat gDNA

Rabbit blood gDNA

Plant leaf gDNA

Optional fragmentation of gDNA

Mammalian sample gDNA

Gram-positive bacterial gDNA

Fish gDNA

Methods for enrichment of polyadenylated RNA molecules

Human cell line gDNA

Avian liver gDNA

Avian gDNA

Avian blood gDNA

This is an Early Access device. For more information about our Early Access programmes, please refer to this article on [product release phases](https://nanoporetech.com/news/news-blog-you-cant-put-label-innovation-or-can-you).

This protocol: - Is for sequencing native RNA - Can be used with total RNA or an enriched sample (e.g. poly(A) tailed or ribo-depleted) as a starting input material - Requires no fragmentation - Takes approximately 140 minutes for library preparation - Is only compatible with RNA flow cells __For Research Use Only__

This protocol: - Is for sequencing native RNA - Can be used with total RNA or an enriched sample (e.g. poly(A) tailed or ribo-depleted) as a starting input material - Requires no fragmentation - Takes approximately 140 minutes for library preparation - Is only compatible with RNA flow cells __For Research Use Only__

This protocol: - Is for selecting RNA targets of your choice for native RNA sequencing - Uses total RNA as a starting input material - Requires no fragmentation - Takes approximately 140 minutes for library preparation __For Research Use Only__

This protocol: - Is for a control experiment using kit-supplied RNA - Sequences native RNA - Requires no fragmentation - Takes approximately 140 minutes for library preparation - Is only compatible with RNA flow cells __For Research Use Only__

This protocol: - is a rapid method to perform sequencing and analysis of *Salmonella*. - uses *Salmonella* colonies from overnight cultures. - includes tagmentation, barcoding and PCR amplification. - enables multiplexing of 1-24 samples. - is compatible with R10.4.1 flow cells. <br> For Research Use Only __This is an Early Access product__ __For more information about our Early Access programmes, please see [this article on product release phases](https://nanoporetech.com/about-us/news/blog-you-cant-put-label-innovation-or-can-you).__

End-to-end method for preparing Chromatin Accessibility libraries. This protocol: - Outlines 6mA tagging - Uses genomic DNA extracted from cell samples - Takes ~340 minutes for sample preparation and ~90 minutes for library preparation. - Requires no PCR - Is compatible with R10.4.1 flow cells __For Research Use Only__

Chemistry Technical Document

Automated end-to-end method using the ElysION device outlining sample extraction, library preparation, sequencing and analysis. This protocol: * Is an automated method using the ElysION device * Uses bacterial or fungi cells * Enables multiplexing of up to 24 samples * Includes DNA fragmentation * Is optimised for high output * Is compatible with R10.4.1 flow cells <br> __For Research Use Only__ This method is used with an Early Access device. For more information about our Early Access programmes, please refer to this article on [product release phases](https://nanoporetech.com/news/news-blog-you-cant-put-label-innovation-or-can-you).

This protocol uses genomic DNA - Hands-on setup time ~30 minutes - Automated run time ~2 hours 40 minutes - Throughput: Process 8–96 samples for singleplex library loading - Compatible with R10.4.1 Flow Cells For Research Use Only

This protocol uses genomic DNA - Automation of library preparation - Increased reproducibility and speed - Reduces human error - High sequencing output - Library preparation time ~1.5 hours hands-on-time and ~3-4 hours automation time - Fragmentation is optional - No PCR required - Multiple samples can be prepared simultaneously - Compatible with R10.4.1 flow cells For Research Use Only

The ElysION MinION Control Unit is an example Compute Unit sold with the ElysION that provides above standard compute requirements for operating and servicing the sequencing device.

This operating manual is for the ElysION: an automated robot for liquid handling, DNA/RNA library preparation, and nanopore sequencing provided by Tecan and Oxford Nanopore Technologies plc (referred to as Oxford Nanopore sequencing herein). The manual contains all the instructions for operating the ElysION safely and for maintaining the device. Read the manual carefully before you perform any work with the ElysION.

The ElysION Data Acquisition Unit is an example Compute Unit sold with the ElysION that provides above standard compute requirements for operating and servicing the sequencing device.