Start-up Checklists
To run a successful Nanopore sequencing experiment in your classroom, you’ll need a combination of basic molecular biology tools, a Nanopore sequencing device, and computational resources. Below is an overview of the materials required, with notes on equipment we generally consider essential. Some specific recommendations also include links to products we have had good success with.
Warning
Check your protocol
These lists are generalizations. Review the specific protocols for your experiments to verify you have the needed supplies. Also note, that PPE recommendations are also specific to the materials and reagents you will use, as well as you institution's laboratory safety guidelines. Please follow those specific guidelines.
Equipment, reagents, supplies, and computer technologies lists
Personal Protective Equipment
| Category | Item | Essential | Notes | Quantities | Recommendations | Price Range |
|---|---|---|---|---|---|---|
| PPE | Disposable gloves | Yes | In addition to reagent contact, recommended to avoid cross contamination | 1 pair per student, lab aide, and instructor per session | Nitrile gloves | $10–$30 per box (100) |
| PPE | Lab coats | Ensures personal and sample safety | 1 per student, lab aide, and instructor | Standard lab coats | $20–$50 per coat | |
| PPE | Safety goggles | May be called for during sample collection or DNA extraction. | 1 per student, lab aide, and instructor | Chemical splash goggles | $5–$20 per goggle | |
| PPE | Waste disposal bags | For safe disposal of biological waste | Varies | Biohazard disposal bags, especially needed if working with cultured microbial samples | $10–$30 per pack |
Molecular Biology Equipment
| Category | Item | Essential | Notes | Quantities | Recommendations | Price Range |
|---|---|---|---|---|---|---|
| Equipment | Micropipettes (1-10 µl, 10-100 µl, 100-1000 µl) | Yes | For precise liquid handling in Nanopore protocols. | 1 set per group + 1 for instructor | Adjustable-volume pipettes from reliable brands like Eppendorf or Gilson. | $50–$300 per pipette |
| Equipment | Thermocycler | Likely | Supports 24+ barcoded samples. Gradient PCR capability is recommended for optimization. | 1 per lab | Bio-Rad or Thermo Fisher systems are suitable for classroom use. Smaller units by miniPCR are inexpensive. | $700–$7,000 |
| Equipment | Microcentrifuge | Yes | For 12-24 1.5 ml tubes. Smaller format for PCR tubes is helpful but not essential. | 1 per lab | Tabletop models from Eppendorf or Thermo Fisher. | $200–$2000 |
| Equipment | Water bath or heat block | Yes | For incubation steps. Hotplates may be used for preparing electrophoresis gels. | 1 per lab (some protocols benefit from additional units) | Heat blocks with adjustable temperature settings are versatile for multiple protocols. | $150–$800 |
| Equipment | Microwave | Hotplates may also be used for preparing electrophoresis gels. | 1 per lab | Standard lab microwave or hotplate. | $50–$150 | |
| Equipment | Electrophoresis tank and power source | Likely | Recommended for checking PCR products and, in some cases, DNA quantity and quality. | 1 set per group or 1 or more communal sets | Compact electrophoresis systems are recommended. See sets such as Carolina and MiniPCR QP-1600-01. | $200–$1000 |
| Equipment | Electrophoresis documentation setup | Likely | UV light source for gel visualization; camera setup (can include a cell phone with proper filters). | 1 per lab | Blue light transilluminators are a safe alternative to UV setups. | $300–$800 |
| Equipment | Glassware for agarose gels (100 ml cylinder, 200 ml Erlenmeyer flask) | Likely | Required for gel preparation. | 1 set per lab | Durable glassware from lab supply companies. | $20–$50 per item |
| Equipment | Magnetic rack | Yes | For magnetic bead cleanups. Should support 1.5–2.0 ml tubes. | 1 per group and 1 or more for lab aid and instructor | Sergilabs offers affordable options. Amazon link | $30–$100 |
| Equipment | Ice bucket(s)/styrofoam containers | Yes | For keeping reagents and samples cold during preparation. | 1 per group and several for lab use | Reusable or disposable options depending on budget. | $10–$50 |
| Equipment | -20°C non-defrosting freezer | Yes | Essential for storing reagents and DNA samples. Low-cost domestic units can be substituted ($200-300) must be non-defrosting. | 1 per lab | Lab-grade non-defrosting freezers are essential to prevent degradation of sensitive materials. | $1,000–$3,000 |
| Equipment | 4°C fridge | Yes | For short-term reagent and sample storage as well as storage of flow cells. Low-cost domestic units can be substituted ($200-300). | 1 per lab | Lab-grade refrigerators preferred for consistency. | $1,000–$2,000 |
| Equipment | Qubit fluorometer | For DNA quantification. Many protocols will work with estimates provided by electrophoresis gel. | 1 per lab (optional) | Thermo Fisher Qubit (Q33238). Thermo Fisher link | ~$4,600 | |
| Equipment | Nanodrop | For DNA quantification. Similar considerations as the Qubit. | 1 per lab (optional) | Thermo Fisher Nanodrop (NDLPLUSGL). Thermo Fisher link | ~$7,200 |
Nanopore Sequencing Equipment
| Category | Item | Essential | Notes | Quantities | Recommendations | Price Range |
|---|---|---|---|---|---|---|
| Sequencing Equipment | MinION sequencer (M1kC or M1kD) | Yes | Portable device capable of generating up to 50 Gb per run. Note: M1kB model is discontinued. | 1 per group or lab | Suitable for a wide range of applications; choose model based on specific needs. | ~$1,000–$2,000*+ |
| Sequencing Equipment | Flongle adapter | Likely | Adapter for MinION or GridION; enables sequencing on Flongle Flow Cells, generating up to 2.8 Gb per run. | 1 per group or lab | Ideal for small-scale, cost-effective sequencing projects. | ~$1,460* - generally available only as part of a starter pack |
| Sequencing Equipment | GridION | High-throughput device; can run up to 5 MinION Flow Cells simultaneously, each generating up to 50 Gb per run. | 1 per lab (if applicable) | Suitable for labs requiring higher throughput and integrated compute capabilities. | ~$67,000*+ | |
| Sequencing Equipment | P2 Solo | Modular device; can run up to 2 PromethION Flow Cells simultaneously, each capable of generating up to 290 Gb per flow cell. Note: P2 and PromethION flow cells are different and not compatible with MinION flowcells. | 1 per lab (if applicable) | Ideal for labs with high-throughput sequencing needs; requires external compute resources. | ~$9,555*+ |
Tip
Educator Discounts*
Prices change frequently, and these prices do not necessarily reflect potential educator discounts as they are offered by Oxford Nanopore.
Nanopore Sequencing Kits
Depending on your application, you will need at least one Nanopore library preparation kit. We feature the following in this guide, see the Nanopore Store for a full product list.
| Category | Item | Essential | Notes | Quantities | Recommendations | Price Range |
|---|---|---|---|---|---|---|
| Sequencing Kits | Ligation Sequencing Kit V14 (SQK-LSK114) | Yes | Flexible method for preparing sequencing libraries from dsDNA, including gDNA, cDNA, or amplicons. Involves end-repair, dA-tailing, and adapter ligation. | 1 per run (6 genomic samples) | Whole-genome sequencing, amplicon sequencing, and cDNA sequencing. | $699* |
| Sequencing Kits | Rapid Barcoding Sequencing Kit 24 V14 (SQK-RBK114.24) | Yes | Enables rapid preparation of up to 24 barcoded sequencing libraries without PCR amplification. Suitable for low-input gDNA. | 1 per run (24 barcoded samples) | DNA barcoding, microbial genomics, small genome sequencing, and amplicon sequencing. | $699* |
| Sequencing Kits | 16S Barcoding Kit 24 V14 (SQK-16S114.24) | Yes | Designed for rapid amplification and sequencing of the 16S rRNA gene, allowing genus-level identification of bacteria. Includes 24 unique barcodes for multiplexing. | 1 per run (24 barcoded samples) | Microbiome analysis and bacterial identification. | $900* |
Tip
*Educator Discounts
Prices change frequently, and these prices do not necessarily reflect potential educator discounts as they are offered by Oxford Nanopore.
Tip
Nanopore Library Prep Kits
We will provide specific recommendations for Nanopore sequencing kits which have their own specific reagents and associated costs. Additional reagents required by the kit incur additional costs.
Molecular Biology Consumables
| Category | Item | Essential | Notes | Quantities | Recommendations | Price Range |
|---|---|---|---|---|---|---|
| Consumables | Micropipette tips (1-10 µl, 10-100 µl, 100-1000 µl) | Yes | Consider filter tips for PCR and/or with precious samples to avoid cross-contamination. | Multiple boxes per lab | Filter tips recommended for sensitive work. | $10–$50 per box |
| Consumables | 0.2 ml PCR tubes | Yes | Essential for PCR workflows. | Multiple packs per lab | High-quality, sterile PCR tubes from trusted brands. | $10–$30 per pack |
| Consumables | 1.5 ml or 1.7 ml microfuge tubes | Yes | Sterile and DNA/DNase-free strongly recommended. | Multiple packs per lab | Brands like Eppendorf or Thermo Fisher offer reliable options. | $10–$30 per pack |
| Consumables | 1.7 ml lo-bind tubes | Many Nanopore protocols call for these. Strongly recommended when working with precious samples. | Multiple packs per lab | Eppendorf LoBind Tubes | ~$50 per box (250) | |
| Consumables | Freezer-safe tape and labels | Yes | For labeling samples stored at -20°C or lower. | Multiple rolls per lab | Freezer-safe tape and lab-specific labels ensure sample integrity. | $5–$20 per roll |
| Consumables | Permanent markers | Yes | Useful for labeling tubes and containers. | Multiple per lab | Choose markers with fade-resistant, waterproof ink. | $1–$5 per marker |
Molecular Biology Reagents
| Category | Item | Essential | Notes | Quantities | Recommendations | Price Range |
|---|---|---|---|---|---|---|
| Reagents | Agarose powder | Likely | For preparing electrophoresis gels. | Multiple packs per lab | Molecular biology grade agarose is recommended. | $50+ per bottle |
| Reagents | DNA loading dye | Likely | Required for visualizing DNA on electrophoresis gels. | 1–2 bottles per lab | Choose dyes compatible with your gel documentation system. | Varies, but inexpensive |
| Reagents | DNA stain | Likely | For staining DNA in gels. Options include SYBR Safe, GelRed, or ethidium bromide (use cautiously). | 1–2 bottles per lab | Invitrogen SYBR Safe is non-toxic; GelRed is safer than ethidium bromide and has good visualization properties. | $100–$300 per bottle |
| Reagents | Buffer solutions (e.g., TAE or TBE) | Likely | For electrophoresis and sample preparation. | Multiple bottles per lab | Purchase premade buffers or prepare stock solutions. | $20–$50 per bottle |
| Reagents | DNA standards for electrophoresis | Yes | For estimating DNA fragment sizes during gel electrophoresis. | 1–2 vials per lab | Use molecular weight ladders appropriate for your protocol, such as 1 kb or 100 bp ladders. | $20–$100 per vial |
| Reagents | Nuclease-free water | Yes | For preparing samples and dilutions. | Multiple bottles per lab | Molecular biology grade water is recommended for all DNA-related protocols. | $50+ depending on quantity |
| Reagents | 200 proof ethanol | Yes | Used in DNA/RNA purification and sample cleanup protocols. | Multiple bottles per lab | Molecular biology grade ethanol ensures no contamination in sensitive workflows. | $50+ depending on quantity |
| Reagents | Isopropanol | Yes | Commonly used in DNA/RNA precipitation protocols. | Multiple bottles per lab | Molecular biology grade isopropanol is preferred for reliable results. | $50+ depending on quantity |
Tip
DNA Extraction Kits
We will provide specific recommendations for DNA extraction kits and protocols which have their own specific reagents and associated costs.
Computers, accessories, software, and online accounts
| Category | Item | Essential | Notes | Quantities | Recommendations | Price Range |
|---|---|---|---|---|---|---|
| Computers and Accessories | Laptop or desktop computer* | Yes | Required for running sequencing software and data analysis tools. | 1 per lab and/or per sequencing device | Mid-range or higher specifications; 16 GB RAM, quad-core processor recommended. | $1,000–$2,800 |
| Computers and Accessories | External storage | Useful for storing large sequencing data files. | Several hundred GB to 1TB+ depending on use | Portable SSDs with fast read/write speeds are ideal. | $100–$500 | |
| Computers and Accessories | Internet connection | Yes | Required for downloading software updates and accessing cloud-based tools. | 1 computer | Stable broadband is sufficient; Wi-Fi or Ethernet compatible. | Varies |
| Software | MinKNOW | Yes | Primary software for operating Oxford Nanopore sequencing devices. | 1 per computer | Comes with Oxford Nanopore devices; ensure latest version is installed. | Free with devices |
| Software | EPI2ME | Likely | Cloud-based data analysis platform for processing sequencing data. | 1 installation per computer | Useful for beginners or labs without bioinformatics expertise. | Free or subscription |
| Online Accounts | Oxford Nanopore account | Yes | Required for purchasing devices, kits, and accessing resources. | 1 per instructor | Sign up through the Oxford Nanopore website. | Free |
| Online Accounts | Cloud storage (e.g., Google Drive, Dropbox) | Useful for sharing and backing up sequencing data. Must have an allocation manager who can share access to their resources. | 1 per lab | Choose a storage platform with adequate space for large datasets. | Free or subscription | |
| Online Accounts | NSF ACCESS-CI | National computing infrastructure for advanced data processing. | Depends on configuration | Apply through ACCESS-CI for computational resources. | Free | |
| Online Accounts | JetStream2 | Cloud computing resource for scientific workflows. Requires an NSF ACCESS-CI account and allocation for at least one account manager; students will not necessarily need their own account. | 1 allocation per instructor (can be used across multiple students/sections) | Apply through JetStream2 for access to cloud-based computation. | Free | |
| Online Accounts | DNA Subway | Educational platform for bioinformatics and genomics analysis. | 1 account per student, instructor, lab aide | Sign up at DNA Subway for classroom-friendly analysis tools. | Free | |
| Online Accounts | CyVerse | Cloud-based platform for managing and analyzing large biological datasets. | 1 account per student, instructor, lab aide | Apply at CyVerse for access to computational and data management tools. | Free or subscription | |
| Online Accounts | Galaxy | Open-source platform for bioinformatics workflows, accessible via a web interface. | 1 account per student, instructor, lab aide | Perform bioinformatics tasks without the need for local installations using Galaxy. | Free |
Tip
Choosing a Computer to Run a MinION Device*
Selecting the right computer for your MinION device is crucial for smooth sequencing and data analysis. The requirements vary slightly depending on the model you're using and the operating system:
For the MinION M1kB
- Operating System: Windows 10 or 11, macOS Monterey (12), Ventura (13), Sonoma (14), or Ubuntu 20.04 or 22.04.
- Processor: Intel or AMD processor with at least 4 cores/8 threads.
- Memory: 8 GB RAM (minimum).
- Storage: 500 GB SSD or higher for managing sequencing data.
- USB Ports: Requires USB 3.0 port.
For the full IT requirements, refer to the MinION M1kB specifications.
For the MinION M1kD
- Operating System: Windows 10 or 11, Ubuntu 20.04 LTS, or macOS 12 (Monterey) or later.
- Processor: Intel or AMD processor with at least 4 cores/8 threads.
- Memory: 16 GB RAM or more for optimal performance.
- Storage: 1 TB SSD or higher to handle large datasets.
- USB Ports: Requires USB-C port.
For the full IT requirements, refer to the MinION M1kD specifications.
General Recommendations
- Portability: A laptop or MacBook is ideal for portability, especially for fieldwork or classroom use.
- Performance: For labs handling high-throughput sequencing, invest in a computer with higher specifications than the minimum.
- External Storage: Consider adding an external SSD to manage and back up sequencing data efficiently.
Choosing the right system ensures reliable performance and smooth operation of your MinION device.
Current best pick - MacBook Pro
While any computer meeting the minimum specifications provided by Oxford Nanopore Technologies will work, we currently recommend the 14-inch MacBook Pro with the M3 chip for its excellent performance and compatibility. This recommendation may be updated as technologies evolve. If you already have access to a computer meeting Nanopore's minimum requirements, it should work just fine.
Recommended Configuration
- Processor: Apple M3 chip with 8-core CPU, 10-core GPU, and 16-core Neural Engine.
- Memory: 24 GB unified memory.
- Storage: 1 TB SSD for managing sequencing data.
- Ports: Two Thunderbolt / USB 4 ports, HDMI port, SDXC card slot, headphone jack, and MagSafe 3 port.
- Operating System: macOS Sonoma (14) or later.
- Display: 14-inch Liquid Retina XDR for clear and detailed data visualization.
Learn more about this MacBook Pro model on the Apple website.
Why We Recommend This MacBook Pro
- Performance: The M3 chip provides robust performance for running sequencing software like MinKNOW and performing bioinformatics analyses.
- Portability: Its compact size and long battery life make it ideal for classroom or fieldwork settings.
- Compatibility: Fully compatible with Oxford Nanopore devices and software, including macOS-supported versions.
- Future-Proofing: With cutting-edge technology, this MacBook is well-suited for evolving software and sequencing demands.
Comments and discussion
See recent comments or start a discussion on our Slack channel.