Resources: Documentation

This is an Early Access device. For Research Use Only

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).

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 __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).

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

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. 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).__

Analysis of cell-free (cf)DNA can be used for a range of uses, including cancer detection and tissue-of-origin analysis. This document is a repository for all of our internally developed methods, know-how documents and information. This will ensure our users can easily access all the required information and our recommended best practices using nanopore sequencing technology for cfDNA.

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 ~60 minutes for library preparation. * requires no PCR * is compatible with R10.4.1 flow cells __For Research Use Only__

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

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

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 __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 __For Research Use Only__

Nanopore-only Microbial Isolate Sequencing Solution (NO-MISS) associated extraction protocols

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 __For Research Use Only__

Nanopore-only Microbial Isolate Sequencing Solution (NO-MISS) associated extraction protocols

Single-cell transcriptomics method: - Requires cDNA amplicons produced using the 10X Genomics Next GEM Single Cell 5' Kit (V2) - Library preparation time ~135 minutes - High output - PCR required For Research Use Only

This guide will help you install, check and configure your PromethION 2 Integrated. For Research Use Only.

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 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 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

Single-cell transcriptomics method: - Requires cDNA amplicons produced using the 10X Genomics Next GEM Single Cell 3' Kit (V3.1) - Library preparation time ~205 minutes - High output - PCR required 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

This protocol: - is for a control experiment using kit-supplied RNA. - sequences native RNA. - requires no fragmentation. - takes ~2 hours for library preparation. 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: - is for selecting RNA targets of your choice for sequencing native RNA. - uses total RNA as starting input material. - requires no fragmentation. - takes ~2 hours for library preparation. 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: - is for sequencing native RNA. - can use total RNA or an enriched sample (e.g. poly(A)+ or ribodepleted) as starting input material. - requires no fragmentation. - takes ~2 hours for library preparation. 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).__

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

Avian liver gDNA

Avian blood gDNA

Rabbit muscle gDNA

Rabbit skin gDNA

Rabbit lung gDNA

Rabbit blood gDNA

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 For Research Use Only

Rabbit fat gDNA

This protocol uses genomic DNA - Very low input requirements (e.g. single cells) - Multiple displacement amplification (MDA) - 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 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 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 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 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 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).__

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 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 ~140 minutes + PCR - includes PCR steps - is compatible with R10.4.1 flow cells For Research Use Only

Requires the PCR Barcoding Expansion (EXP-PBC001 or EXP-PBC096) with the Ligation Sequencing Kit V14 (SQK-LSK114) - This protocol barcodes gDNA or amplicons - Library preparation time ~150 minutes + PCR - High yield - Uses up to 96 barcodes - Includes PCR steps - Compatible with R10.4.1 flow cells For Research Use Only

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

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

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

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).__

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

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 uses N50 of 30 kb genomic DNA extracted from human cell lines * Sample preparation time: ~320 minutes and library preparation time: ~60 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: ~60 minutes - Data analysis: 1-2 hours - No PCR - Compatible with R10.4.1 flow cells For Research Use Only

This guide will help you install, check and configure your PromethION 2 Solo. Our PromethION 2 Solo FAQs are located [here](https://nanoporetech.com/support/devices/p2-solo). 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

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 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

Automated gDNA extraction from dry blood spots (FTA cards)

Extracting and preparing DNA from brain tissue for Oxford Nanopore Sequencing

This protocol uses Lambda control DNA - Library preparation time ~60 minutes - Fragmentation optional - No PCR - Compatible with R10.4.1 flow cells For Research Use Only

This protocol uses genomic DNA - Library preparation time ~60 minutes - Fragmentation optional - No PCR - Compatible with R10.4.1 flow cells For Research Use Only

This protocol uses amplicon DNA - Library preparation time ~60 minutes - Fragmentation optional - No PCR For Research Use Only

This protocol uses genomic DNA - Library preparation time ~120 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

Environmental water (eDNA)

Human blood cell-free DNA (cfDNA)

Plasmid DNA

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

Size selection

Optional fragmentation of gDNA

Mammalian sample gDNA

Enrichment of polyadenylated RNA molecules

Restriction enzyme Pore-C sample preparation and extraction protocols

Plant leaf gDNA

Human cell line gDNA

Avian gDNA

Gram-positive bacterial gDNA

Stool pellet gDNA

Yeast cell culture RNA

Salmon sample gDNA

Fish gDNA

Yeast DNA

Human cell line RNA

Western clawed frog (Xenopus tropicalis) muscle DNA

Worm (Caenorhabditis elegans) DNA

Reptile tissue DNA

Human saliva DNA

Arabidopsis (Arabidopsis thaliana LEr) leaf RNA

Whole genome colony PCR

Agarose plug DNA

Worm (Caenorhabditis elegans) RNA

Gram-negative bacterial DNA

Soil DNA

Fruit fly (Drosophila melanogaster) RNA

Yeast DNA (Community-developed)

FFPE human cell DNA

Fruit fly (Drosophila melanogaster) DNA

Influenza A RNA

Mycobacterium tuberculosis DNA

Human blood RNA

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

Button mushroom (Agaricus bisporus) DNA

For Research Use Only.

For Research Use Only

This document will help you to install, check and configure your Q system GridION™.

MinKNOW - the MinION control software. For Research Use Only.

For Research Use Only

This document will help you to install, check and configure your GridION™. Our device FAQs are located [here](https://help.nanoporetech.com/en/collections/3738235-devices). For Research Use Only.

This guide will help you install, check and configure your PromethION 24, PromethION 48 or PromethION 24/48 A-Series. Our PromethION 24/48 FAQs are located [here](https://help.nanoporetech.com/en/collections/3738263-promethion). For Research Use Only.

For Research Use Only

Checking the MinION™ Mk1B has been assembled, installed and set up correctly. Our device FAQs are located [here](https://help.nanoporetech.com/en/collections/3738235-devices). For Research Use Only

For Research Use Only

Instructions for working with MinKNOW. If using for the first time, please refer to the user manual for your device. For Research Use Only

For Research Use Only

This user manual will enable the user of the MinION Mk1C to: - Power up and down the device - Learn the shortcuts enabled by touchscreen in the MinION Mk1C Graphical User Interface (GUI) - Use the Host Settings for system software configuration - Access the device remotely for control of MinKNOW and to transfer data on Windows, macOS and Linux computers - Access the device through SecureShell/the Terminal for data transfer and device configuration Our device FAQs are located [here](https://help.nanoporetech.com/en/collections/3738235-devices). For Research Use Only

For Research Use Only

This info sheet highlights the application and advantages of chromatin conformation capture with nanopore sequencing, known as Pore-C. The restriction enzyme Pore-C (RE-Pore-C) is intended for the manipulation of cell or nuclei suspensions to capture three-dimensional interactions of DNA within chromatin. When sequenced on Oxford Nanopore Technologies sequencing platforms, Pore-C can enable native sequencing of chromatin conformation capture extracts whilst retaining DNA base modifications. The RE-Pore-C protocol has been developed using human cell line culture, although can also be used in conjunction with other sample types, including animal tissue and insects prepared following the relevant recommended Pore-C sample preparation procedure. In addition, there is a separate protocol for Plant Pore-C which differs from the RE-Pore-C protocol to accommodate plant samples. Protocols are located in the [Extraction protocols](https://community.nanoporetech.com/docs/prepare/extraction_protocols) section of the Nanopore Community. For Research Use Only.