Ligation sequencing gDNA V14 — whole genome amplification (SQK-LSK114)
Protocol
Ligation sequencing gDNA V14 — whole genome amplification (SQK-LSK114) VWAL_9192_v114_revE_26Jul2023
- 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
FOR RESEARCH USE ONLY
Contents
Introduction to the protocol
Library preparation
- 3. Whole genome amplification
- 4. DNA repair and end-prep
- 5. Adapter ligation and clean-up
- 6. Priming and loading the MinION and GridION Flow Cell
Sequencing and data analysis
Troubleshooting
Overview
- 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
1. Overview of the protocol
Introduction to the whole genome amplification protocol
This protocol describes how to carry out whole genome amplification (WGA) of genomic DNA using the Ligation Sequencing Kit (SQK-LSK114) and the QIAGEN REPLI-g Midi kit.
Please note, the whole genome amplification step described in this protocol is based off the methods described in the REPLI-g® Mini/Midi Handbook. Please refer to the QIAGEN documentation for additional information.
This protocol uses the multiple displacement amplification (MDA) method with the QIAGEN kit to amplify as little as 50 pg of bacterial DNA to yield up to 40 ug DNA. T7 Endonuclease I treatment is performed to resolve the hyperbranched structure of the WGA product and to improve read quality (Qscore) and flow cell output. It is important to note, however, that by using this method some amplification bias can be introduced in the MDA reaction.
Please note, using this protocol will result in shorter fragment lengths and lower flow cell output than preparing a DNA library using the standard Ligation Sequencing DNA V14 protocol.
Please refer to our Sequencing products of multiple displacement amplification (MDA) know-how document for more information on the available methods.
Steps in the sequencing workflow:
Prepare for your experiment
You will need to:
- Extract your DNA, and check its length, quantity and purity. The quality checks performed during the protocol are essential in ensuring experimental success.
- Ensure you have your sequencing kit, the correct equipment and third-party reagents
- Download the software for acquiring and analysing your data
- Check your flow cell to ensure it has enough pores for a good sequencing run
Library preparation
You will need to:
- Amplify the genomic DNA using random hexamer primers
- Digest the amplified DNA with T7 Endonuclease I to remove branching, and size-select for longer fragments using AMPure XP beads
- Prepare the DNA ends for adapter attachment
- Attach sequencing adapters supplied in the kit to the DNA ends
- Prime the flow cell, and load your DNA library into the flow cell
Sequencing and analysis
You will need to:
- Start a sequencing run using the MinKNOW software, which will collect raw data from the device and convert it into basecalled reads
- Start the EPI2ME software and select a workflow for further analysis (this step is optional)
Increasing flow cell output with PCR amplification
In instances where flow cell output is reduced when sequencing the products of MDA using the ligation-based protocol (<10 Gb from a MinION flow cell), we have found that performing a PCR amplification using the Rapid PCR Barcoding Kit 24 V14 (SQK-RPB114.24) can recover flow cell output.
We recommend taking 5 ng of the MDA amplified sample from the whole genome amplification step described in this protocol and using it as input for the Rapid sequencing DNA - PCR Barcoding Kit 24 V14 (SQK-RPB114.24) protocol to perform additional PCR amplification.
Please note, amplification bias could potentially be exacerbated with additional PCR, and some GC-bias can be introduced, leading to a slight reduction in coverage at the extremes of GC-content.
For more information refer to the info sheet: Sequencing products of multiple displacement amplification (MDA).
IMPORTANT
This protocol was developed using E. coli gDNA. If using a different type of sample, please refer to the QIAGEN protocol for advice on how to modify the sample prep accordingly.
IMPORTANT
Compatibility of this protocol
This protocol should only be used in combination with:
- Ligation Sequencing Kit V14 (SQK-LSK114)
- Control Expansion (EXP-CTL001)
- R10.4.1 flow cells (FLO-MIN114)
- Flow Cell Wash Kit (EXP-WSH004)
- MinION Mk1B - MinION Mk1B IT requirements document
- MinION Mk1C - MinION Mk1C IT requirements document
- GridION - GridION IT requirements document
2. Equipment and consumables
Materials
- 50 pg high molecular weight genomic DNA
- Ligation Sequencing Kit V14 (SQK-LSK114)
- REPLI-g® Single Cell Kit (QIAGEN, cat # 150343)
Consumables
- MinION and GridION Flow Cell
- Agencourt AMPure XP beads (Beckman Coulter, A63881)
- NEBNext® Companion Module v2 for Oxford Nanopore Technologies® Ligation Sequencing (NEB, E7672S or E7672L)
- Salt-T4® DNA Ligase (NEB, M0467)
- Covaris g-TUBE
- 2 ml Eppendorf DNA LoBind tubes
- 1.5 ml Eppendorf DNA LoBind tubes
- 0.2 ml thin-walled PCR tubes
- Nuclease-free water (e.g. ThermoFisher, AM9937)
- Freshly prepared 80% ethanol in nuclease-free water
- T7 Endonuclease I (NEB, cat # M0302)
- TE buffer: 10 mM Tris (pH 8.0), 0.1 mM EDTA
- PEG 8000, 50% w/v (Rigaku Reagents, 25322-68-3)
- 0.5 M EDTA, pH 8 (Thermo Scientific, R1021)
- 5 M NaCl (Sigma, 71386)
- 1 M Tris-HCl pH 8.0 (Thermo Scientific, 15893661)
- Bovine Serum Albumin (BSA) (50 mg/ml) (e.g Invitrogen™ UltraPure™ BSA 50 mg/ml, AM2616)
Equipment
- MinION or GridION device
- MinION and GridION Flow Cell Light Shield
- Hula mixer (gentle rotator mixer)
- Magnetic rack, suitable for 1.5 ml Eppendorf tubes
- Microfuge
- Vortex mixer
- Heating block at 37°C capable of taking 1.5 ml tubes
- Thermal cycler
- Ice bucket with ice
- Timer
- P1000 pipette and tips
- P200 pipette and tips
- P100 pipette and tips
- P20 pipette and tips
- P10 pipette and tips
- P2 pipette and tips
- Qubit fluorometer (or equivalent for QC check)
Optional equipment
- Standard gel electrophoresis equipment
- Agilent Bioanalyzer (or equivalent)
- Eppendorf 5424 centrifuge (or equivalent)
For this protocol, you will need 50 pg high molecular weight genomic DNA.
Input DNA
How to QC your input DNA
It is important that the input DNA meets the quantity and quality requirements. Using too little or too much DNA, or DNA of poor quality (e.g. highly fragmented or containing RNA or chemical contaminants) can affect your library preparation.
For instructions on how to perform quality control of your DNA sample, please read the Input DNA/RNA QC protocol.
Chemical contaminants
Depending on how the DNA is extracted from the raw sample, certain chemical contaminants may remain in the purified DNA, which can affect library preparation efficiency and sequencing quality. Read more about contaminants on the Contaminants page of the Community.
NEBNext® Companion Module v2 for Oxford Nanopore Technologies® Ligation Sequencing
We recommend buying the NEBNext® Companion Module v2 for Oxford Nanopore Technologies® Ligation Sequencing (catalogue number E7672S or E7672L), which contains all the NEB reagents needed for use with the Ligation Sequencing Kit.
The previous version, NEBNext® Companion Module for Oxford Nanopore Technologies® Ligation Sequencing (NEB, E7180S or E7180L) is compatible, but the recommended v2 module offers more efficient dA-tailing and ligation, a result of the FFPEv2 DNA Repair Buffer and Salt-T4 DNA Ligase, respectively.
A marked cost saving per sample preparation is also realised when using the v2 module.
Please note, for our amplicon protocols, NEBNext FFPE DNA Repair Mix is not required and purchasing the required reagents separately is more cost effective.
Third-party reagents
We have validated and recommend the use of all the third-party reagents used in this protocol. Alternatives have not been tested by Oxford Nanopore Technologies.
For all third-party reagents, we recommend following the manufacturer's instructions to prepare the reagents for use.
Check your flow cell
We highly recommend that you check the number of pores in your flow cell prior to starting a sequencing experiment. This should be done within three months of purchasing for MinION/GridION/PromethION or within four weeks of purchasing Flongle Flow Cells. Oxford Nanopore Technologies will replace any flow cell with fewer than the number of pores in the table below, when the result is reported within two days of performing the flow cell check, and when the storage recommendations have been followed. To do the flow cell check, please follow the instructions in the Flow Cell Check document.
| Flow cell | Minimum number of active pores covered by warranty |
|---|---|
| Flongle Flow Cell | 50 |
| MinION/GridION Flow Cell | 800 |
| PromethION Flow Cell | 5000 |
IMPORTANT
AMPure XP Beads
Within the Ligation Sequencing Kit 24 V14 (SQK-LSK114), AMPure XP Beads (AXP) are supplied at the volume needed to complete the "DNA repair and end-prep" and "adapter ligation and clean-up" steps of the protocol.
However, extra AMPure XP Beads are required for the "whole genome amplification" step of the protocol.
IMPORTANT
We strongly recommend using the Ligation Buffer (LNB) supplied in the Ligation Sequencing Kit V14 rather than any third-party ligase buffers to ensure high ligation efficiency of the Ligation Adapter (LA).
IMPORTANT
Ligation Adapter (LA) included in this kit and protocol is not interchangeable with other sequencing adapters.
Ligation Sequencing Kit V14 (SQK-LSK114) contents
Note: We are in the process of reformatting our kits with single-use tubes into a bottle format.
Single-use tubes format: 
Bottle format: 
Note: This Product Contains AMPure XP Reagent Manufactured by Beckman Coulter, Inc. and can be stored at -20°C with the kit without detriment to reagent stability.
Note: The DNA Control Sample (DCS) is a 3.6 kb standard amplicon mapping the 3' end of the Lambda genome.
3. Whole genome amplification
Materials
- 50 pg high molecular weight genomic DNA
- REPLI-g® Single Cell Kit (QIAGEN, cat # 150343)
Consumables
- Nuclease-free water (e.g. ThermoFisher, AM9937)
- 2 ml Eppendorf DNA LoBind tubes
- 1.5 ml Eppendorf DNA LoBind tubes
- 0.2 ml thin-walled PCR tubes
- T7 Endonuclease I (NEB, cat # M0302)
- Agencourt AMPure XP beads (Beckman Coulter, A63881)
- Freshly prepared 80% ethanol in nuclease-free water
- TE buffer: 10 mM Tris (pH 8.0), 0.1 mM EDTA
- PEG 8000, 50% w/v (Rigaku Reagents, 25322-68-3)
- 0.5 M EDTA, pH 8 (Thermo Scientific, R1021)
- 5 M NaCl (Sigma, 71386)
- 1 M Tris-HCl pH 8.0 (Thermo Scientific, 15893661)
Equipment
- P1000 pipette and tips
- P200 pipette and tips
- P100 pipette and tips
- P10 pipette and tips
- P2 pipette and tips
- Thermal cycler
- Hula mixer (gentle rotator mixer)
- Magnetic rack, suitable for 1.5 ml Eppendorf tubes
- Ice bucket with ice
- Qubit fluorometer (or equivalent for QC check)
Thaw the REPLI-g sc DNA Polymerase on ice, mix well by pipetting and spin down. Store on ice until ready to use.
Prepare the DNA in nuclease-free water.
- Transfer 50 pg genomic DNA into a clean 0.2 ml thin-walled PCR tube.
- Adjust the volume to 4 μl with nuclease-free water.
- Mix thoroughly by inversion and gently flicking to avoiding unwanted shearing.
- Spin down briefly in a microfuge.
Reconstitute the Buffer DLB from the QIAGEN REPLI-g Single Cell kit as follows:
- Add 500 µl of nuclease-free water to the Buffer DLB tube.
- Thoroughly mix by vortexing and briefly spin down.
Note: According to the manufacturers, the reconstituted Buffer DLB can be stored for up to 6 months at -20°C.
In a clean 1.5 ml Eppendorf DNA LoBind tube, prepare sufficient Buffer D2 for the total number of reactions required as follows:
| Reagent | Volume for 4 samples | Volume for 12 samples | Volume for 24 samples |
|---|---|---|---|
| DTT, 1M | 1 µl | 3 µl | 6 µl |
| Reconstituted Buffer DLB | 11 µl | 33 µl | 66 µl |
| Total | 12 µl | 36 µl | 72 µl |
Note: The REPLI-g® Mini/Midi Handbook recommends preparing a stock of Buffer D2 minimise risk of error when pipetting small volumes. According to the manufacturers, the prepared Buffer D2 can be stored for up to 3 months at -20°C.
Add 3 µl of prepared Buffer D2 to the gDNA input sample in the 0.2 ml thin-walled PCR tube.
Mix gently by flicking the tube and spin down.
Incubate the reaction at 65°C for 10 minutes.
Add 3 µl of of Stop Solution to the denatured DNA sample tube. Mix by flicking the tube, briefly spin down and place on ice.
In a clean 1.5 ml Eppendorf DNA LoBind tube placed on ice, prepare the master mix as follows:
Pipette mix 10-20 times between each addition.
| Reagent | Volume | | --- | --- | --- | --- | | Nuclease-free water | 9 µl | | REPLI-g sc Reaction Buffer | 29 µl | | REPLI-g sc DNA Polymerase | 2 µl | | Total | 40 µl |
Mix thoroughly by pipetting and briefly spin down before storing the master mix on ice.
Combine the following reagents in the same 0.2 ml thin-walled PCR tube containing the sample:
| Reagent | Volume |
|---|---|
| Denatured DNA sample (from previous step) | 10 µl |
| Prepared master mix | 40 µl |
| Total | 50 µl |
Mix gently by flicking the tube and spin down.
Incubate the reaction for 2 hours at 30°C and 3 minutes at 65°C using a thermal cycler.
Transfer the sample to a clean 1.5 ml Eppendorf DNA LoBind tube.
Resuspend the AMPure XP beads by vortexing.
Add 90 µl of resuspended AMPure XP beads to the amplification reaction and mix by pipetting.
Incubate on a Hula mixer (rotator mixer) for 5 minutes at room temperature.
Prepare 500 μl of 80% ethanol in nuclease-free water.
Spin down the sample and pellet on a magnet. Keep the tube on the magnet, and pipette off the supernatant when clear and colourless.
Keep the tube on the magnet and wash the beads with 200 µl of freshly prepared 80% ethanol without disturbing the pellet. Remove the ethanol using a pipette and discard.
Spin down and place the tube back on the magnet. Pipette off any residual ethanol. Allow to dry for ~30 seconds, but do not dry the pellet to the point of cracking.
Remove the tube from the magnetic rack and resuspend pellet in 100 µl nuclease-free water. Incubate for 2 minutes at room temperature.
Pellet the beads on a magnet until the eluate is clear and colourless.
Remove and retain 100 µl of eluate in a clean 1.5 ml Eppendorf DNA LoBind tube.
CHECKPOINT
Quantify 1 µl of the eluted sample using a Qubit fluorometer.
Prepare your amplified DNA sample as follows:
- Transfer 1.5 µg of amplified DNA into a clean 0.2 ml thin-walled PCR tube.
- Adjust the volume to 24 μl with nuclease-free water.
- Mix thoroughly by inversion and gently flicking to avoiding unwanted shearing.
- Spin down briefly in a microfuge.
Prepare the following reaction in the 0.2 ml thin-walled PCR tube containing the sample by adding the reagents in the following order:
| Reagent | Volume |
|---|---|
| 1.5 µg of amplified DNA (from previous step) | 24 µl |
| NEBuffer 2 | 3 µl |
| T7 Endonuclease I | 3 µl |
| Total | 30 µl |
Thoroughly mix the reaction by gently pipetting and briefly spinning down.
Incubate the reaction for 60 minutes at 37°C.
Prepare the Custom buffer with beads as follows:
- Prepare the Custom buffer mix in a clean 2 ml Eppendorf DNA LoBind tube:
| Reagent | Volume |
|---|---|
| 1 M Tris-HCl | 20 μl |
| 0.5 M EDTA pH 8 | 4 μl |
| 5 M NaCl | 640 μl |
| PEG 8000 | 440 μl |
| Nuclease-free water | 888 μl |
| Total | 1992 μl |
- Mix the Custom buffer thoroughly by pipetting.
- Resuspend the AMPure XP beads by vortexing.
- Prepare two 1.5 ml Eppendorf DNA LoBind tubes to contain 1 ml of resuspended AMPure XP beads each.
- Pellet the beads in both tubes on a magnet. Keeping the tubes on the magnet, pipette off the supernatants.
- Remove both tubes from the magnet and resuspend the beads in each tube with 1 ml of nuclease-free water. Return the tubes to the magnet and allow the beads to pellet. Pipette off the water and discard.
- Repeat the previous step.
- Spin down and place the tubes back on the magnet. Pipette off any residual water.
- Resuspend both pellets in 200 ul of Custom Buffer. Transfer the full volume of both tubes of resuspended beads to the remaining Custom buffer in the 2 ml Eppendorf LoBind DNA tube.
- Mix the Custom buffer with beads thoroughly by pipetting.
Prepare the amplified DNA sample as follows:
- Transfer the 30 µl of amplified DNA sample into a clean 1.5 ml Eppendorf DNA LoBind tube.
- Adjust the volume to 50 μl with TE buffer, pH 8.
- Mix thoroughly by inversion and gently flicking to avoiding unwanted shearing.
- Spin down briefly in a microfuge.
Add 35 µl of the Custom buffer with beads to the DNA sample, and mix by flicking the tube.
Note: Thoroughly mix the Custom buffer by pipetting prior to use to ensure the beads are fully resuspended.
Incubate on a Hula mixer (rotator mixer) for 10 minutes at room temperature. This step may be extended to 20 minutes if a slightly higher DNA recovery yield is desired.
Prepare 500 μl of 80% ethanol in nuclease-free water.
Spin down the sample and pellet on a magnet until supernatant is clear and colourless. Keep the tube on the magnet, and pipette off the supernatant.
Keep the tube on the magnet and wash the beads with 200 µl of freshly prepared 80% ethanol without disturbing the pellet. Remove the ethanol using a pipette and discard.
Repeat the previous step.
Spin down and place the tube back on the magnet. Pipette off any residual supernatant. Allow to dry for ~30 seconds, but do not dry the pellet to the point of cracking.
Remove the tube from the magnetic rack and resuspend pellet in 49 µl nuclease-free water. Incubate for 1 minute at 50°C, and then for 5 minutes at room temperature.
Pellet the beads on a magnet until the eluate is clear and colourless.
Remove and retain 49 µl of eluate into a clean 1.5 ml Eppendorf DNA LoBind tube.
CHECKPOINT
Quantify 1 µl of DNA using a Qubit fluorometer - recovery aim ~700 ng.
END OF STEP
Take forward approximately 700 ng of DNA in 48 µl into the DNA repair and end-prep step. However, at this point it is also possible to store the sample at 4°C overnight.
TIP
Increasing flow cell output with PCR amplification using the Rapid PCR Barcoding Kit 24 V14 (SQK-RPB114.24)
If you have obtained low DNA recovery following the whole genome amplification step, or have previously performed the experiment and observed low flow cell output, please consider performing a PCR amplification of your MDA products using the Rapid PCR Barcoding Kit 24 V14 (SQK-RPB114.24).
We recommend taking 5 ng of the MDA amplified sample from this step of the protocol and using it as the input for the Rapid sequencing DNA - PCR Barcoding Kit 24 V14 (SQK-RPB114.24) protocol.
4. DNA repair and end-prep
Materials
- Amplified DNA in 48 µl nuclease-free water
- AMPure XP Beads (AXP)
Consumables
- NEBNext® FFPE DNA Repair Mix (M6630) from the NEBNext® Companion Module v2 (NEB, E7672S or E7672L)
- NEBNext® Ultra II End Prep Enzyme Mix (E7646) from the NEBNext® Companion Module v2 (NEB, E7672S or E7672L)
- NEBNext® FFPE DNA Repair Buffer v2 (E7363) from the NEBNext® Companion Module v2 (NEB, E7672S or E7672L)
- Qubit dsDNA HS Assay Kit (Invitrogen, Q32851)
- Nuclease-free water (e.g. ThermoFisher, AM9937)
- Freshly prepared 80% ethanol in nuclease-free water
- Qubit™ Assay Tubes (Invitrogen, Q32856)
- 0.2 ml thin-walled PCR tubes
- 1.5 ml Eppendorf DNA LoBind tubes
Equipment
- P1000 pipette and tips
- P100 pipette and tips
- P10 pipette and tips
- Microfuge
- Thermal cycler
- Hula mixer (gentle rotator mixer)
- Magnetic rack
- Ice bucket with ice
Optional equipment
- Qubit fluorometer (or equivalent for QC check)
TIP
We recommend using the NEBNext® Companion Module v2 for Oxford Nanopore Technologies® Ligation Sequencing (catalogue number E7672S or E7672L), which contains all the NEB reagents needed for use with the Ligation Sequencing Kit.
The previous version, NEBNext® Companion Module for Oxford Nanopore Technologies® Ligation Sequencing (NEB, E7180S or E7180L) is also compatible, but the recommended v2 module offers more efficient dA-tailing and ligation.
CHECKPOINT
Check your flow cell.
We recommend performing a flow cell check before starting your library prep to ensure you have a flow cell with enough pores for a good sequencing run.
See the flow cell check instructions in the MinKNOW protocol for more information.
Prepare the NEB reagents in accordance with manufacturer’s instructions, and place on ice.
For optimal performance, NEB recommend the following:
Thaw all reagents on ice.
Flick and/or invert the reagent tubes to ensure they are well mixed.
Note: Do not vortex the FFPE DNA Repair Mix or Ultra II End Prep Enzyme Mix.Always spin down tubes before opening for the first time each day.
Vortex the FFPE DNA Repair Buffer v2, or the NEBNext FFPE DNA Repair Buffer and Ultra II End Prep Reaction Buffer to ensure they are well mixed.
Note: These buffers may contain a white precipitate. If this occurs, allow the mixture(s) to come to room temperature and pipette the buffer several times to break up the precipitate, followed by a quick vortex to mix.The FFPE DNA Repair Buffer may have a yellow tinge and is fine to use if yellow.
In a 0.2 ml thin-walled PCR tube, mix the following:
Between each addition, pipette mix 10-20 times.
| Reagent | Volume |
|---|---|
| Amplified DNA | 48 µl |
| NEBNext FFPE DNA Repair Buffer v2 | 7 µl |
| NEBNext FFPE DNA Repair Mix | 2 µl |
| Ultra II End-prep Enzyme Mix | 3 µl |
| Total | 60 µl |
If using the previous version of the NEBNext® Companion Module for Oxford Nanopore Technologies® Ligation Sequencing (NEB, E7180S or E7180L):
Between each addition, pipette mix 10-20 times.
| Reagent | Volume |
|---|---|
| Amplified DNA | 48 µl |
| NEBNext FFPE DNA Repair Buffer | 3.5 µl |
| NEBNext FFPE DNA Repair Mix | 2 µl |
| Ultra II End-prep Reaction Buffer | 3.5 µl |
| Ultra II End-prep Enzyme Mix | 3 µl |
| Total | 60 µl |
Thoroughly mix the reaction by gently pipetting and briefly spinning down.
Using a thermal cycler, incubate at 20°C for 5 minutes and 65°C for 5 minutes.
Resuspend the AMPure XP Beads (AXP) by vortexing.
Transfer the DNA sample to a clean 1.5 ml Eppendorf DNA LoBind tube.
Add 60 µl of resuspended the AMPure XP Beads (AXP) to the end-prep reaction and mix by flicking the tube.
Incubate on a Hula mixer (rotator mixer) for 5 minutes at room temperature.
Prepare 500 μl of fresh 80% ethanol in nuclease-free water.
Spin down the sample and pellet on a magnet until supernatant is clear and colourless. Keep the tube on the magnet, and pipette off the supernatant.
Keep the tube on the magnet and wash the beads with 200 µl of freshly prepared 80% ethanol without disturbing the pellet. Remove the ethanol using a pipette and discard.
Repeat the previous step.
Spin down and place the tube back on the magnet. Pipette off any residual ethanol. Allow to dry for ~30 seconds, but do not dry the pellet to the point of cracking.
Remove the tube from the magnetic rack and resuspend the pellet in 61 µl nuclease-free water. Incubate for 2 minutes at room temperature.
Pellet the beads on a magnet until the eluate is clear and colourless, for at least 1 minute.
Remove and retain 61 µl of eluate into a clean 1.5 ml Eppendorf DNA LoBind tube.
CHECKPOINT
Quantify 1 µl of eluted sample using a Qubit fluorometer.
END OF STEP
Take forward the repaired and end-prepped DNA into the adapter ligation step. However, at this point it is also possible to store the sample at 4°C overnight.
5. Adapter ligation and clean-up
Materials
- Ligation Adapter (LA)
- Ligation Buffer (LNB)
- Short Fragment Buffer (SFB)
- AMPure XP Beads (AXP)
- Elution Buffer (EB)
Consumables
- Salt-T4® DNA Ligase (NEB, M0467)
- 1.5 ml Eppendorf DNA LoBind tubes
- Qubit dsDNA HS Assay Kit (Invitrogen, Q32851)
- Qubit™ Assay Tubes (Invitrogen, Q32856)
Equipment
- Magnetic rack
- Microfuge
- Vortex mixer
- P1000 pipette and tips
- P100 pipette and tips
- P20 pipette and tips
- P10 pipette and tips
- Qubit fluorometer (or equivalent for QC check)
TIP
We recommend using the Salt-T4® DNA Ligase (NEB, M0467).
Salt-T4® DNA Ligase (NEB, M0467) can be bought separately or is provided in the NEBNext® Companion Module v2 for Oxford Nanopore Technologies® Ligation Sequencing (catalogue number E7672S or E7672L).
The Quick T4 DNA Ligase (NEB, E6057) available in the previous version NEBNext® Companion Module for Oxford Nanopore Technologies® Ligation Sequencing (NEB, E7180S or E7180L) is also compatible, but the new recommended reagent offers more efficient and ligation.
IMPORTANT
Although third-party ligase products may be supplied with their own buffer, the ligation efficiency of the Ligation Adapter (LA) is higher when using the Ligation Buffer (LNB) supplied in the Ligation Sequencing Kit.
Spin down the Ligation Adapter (LA) and Salt-T4® DNA Ligase, and place on ice.
Thaw Ligation Buffer (LNB) at room temperature, spin down and mix by pipetting. Due to viscosity, vortexing this buffer is ineffective. Place on ice immediately after thawing and mixing.
Thaw the Elution Buffer (EB) at room temperature and mix by vortexing. Then spin down and place on ice.
Thaw the Short Fragment Buffer (SFB) at room temperature and mix by vortexing. Then spin down and place on ice.
In a 1.5 ml Eppendorf DNA LoBind tube, mix in the following order:
Between each addition, pipette mix 10-20 times.
| Reagent | Volume |
|---|---|
| DNA sample from the previous step | 60 µl |
| Ligation Adapter (LA) | 5 µl |
| Ligation Buffer (LNB) | 25 µl |
| Salt-T4® DNA Ligase | 10 µl |
| Total | 100 µl |
Thoroughly mix the reaction by gently pipetting and briefly spinning down.
Incubate the reaction for 10 minutes at room temperature.
Resuspend the AMPure XP beads (AXP) by vortexing.
Add 40 µl of resuspended AMPure XP Beads (AXP) to the reaction and mix by flicking the tube.
Incubate on a Hula mixer (rotator mixer) for 5 minutes at room temperature.
Spin down the sample and pellet on a magnet. Keep the tube on the magnet, and pipette off the supernatant when clear and colourless.
Wash the beads by adding 250 μl of Short Fragment Buffer (SFB). Flick the beads to resuspend, spin down, then return the tube to the magnetic rack and allow the beads to pellet. Remove the supernatant using a pipette and discard.
Note: Take care when removing the supernatant, the viscosity of the buffer can contribute to loss of beads from the pellet.
Repeat the previous step.
Spin down and place the tube back on the magnet. Pipette off any residual supernatant. Allow to dry for ~30 seconds, but do not dry the pellet to the point of cracking.
Remove the tube from the magnetic rack and resuspend the pellet in 15 µl Elution Buffer (EB). Spin down and incubate for 10 minutes at room temperature. For high molecular weight DNA, incubating at 37°C can improve the recovery of long fragments.
Pellet the beads on a magnet until the eluate is clear and colourless, for at least 1 minute.
Remove and retain 15 µl of eluate containing the DNA library into a clean 1.5 ml Eppendorf DNA LoBind tube.
Dispose of the pelleted beads
CHECKPOINT
Quantify 1 µl of eluted sample using a Qubit fluorometer.
Depending on your DNA library fragment size, prepare your final library in 12 µl of Elution Buffer (EB).
| Fragment library length | Flow cell loading amount |
|---|---|
| Very short (<1 kb) | 100 fmol |
| Short (1-10 kb) | 35–50 fmol |
| Long (>10 kb) | 300 ng |
Note: If the library yields are below the input recommendations, load the entire library.
If required, we recommend using a mass to mol calculator such as the NEB calculator.
END OF STEP
The prepared library is used for loading into the flow cell. Store the library on ice or at 4°C until ready to load.
TIP
Library storage recommendations
We recommend storing libraries in Eppendorf DNA LoBind tubes at 4°C for short-term storage or repeated use, for example, re-loading flow cells between washes. For single use and long-term storage of more than 3 months, we recommend storing libraries at -80°C in Eppendorf DNA LoBind tubes.
6. Priming and loading the MinION and GridION Flow Cell
Materials
- Flow Cell Flush (FCF)
- Flow Cell Tether (FCT)
- Library Solution (LIS)
- Library Beads (LIB)
- Sequencing Buffer (SB)
Consumables
- MinION and GridION Flow Cell
- 1.5 ml Eppendorf DNA LoBind tubes
- Nuclease-free water (e.g. ThermoFisher, AM9937)
- Bovine Serum Albumin (BSA) (50 mg/ml) (e.g Invitrogen™ UltraPure™ BSA 50 mg/ml, AM2616)
Equipment
- MinION or GridION device
- MinION and GridION Flow Cell Light Shield
- P1000 pipette and tips
- P100 pipette and tips
- P20 pipette and tips
- P10 pipette and tips
IMPORTANT
Please note, this kit is only compatible with R10.4.1 flow cells (FLO-MIN114).
TIP
Priming and loading a flow cell
We recommend all new users watch the 'Priming and loading your flow cell' video before your first run.
Thaw the Sequencing Buffer (SB), Library Beads (LIB) or Library Solution (LIS, if using), Flow Cell Tether (FCT) and Flow Cell Flush (FCF) at room temperature before mixing by vortexing. Then spin down and store on ice.
IMPORTANT
For optimal sequencing performance and improved output on MinION R10.4.1 flow cells (FLO-MIN114), we recommend adding Bovine Serum Albumin (BSA) to the flow cell priming mix at a final concentration of 0.2 mg/ml.
Note: We do not recommend using any other albumin type (e.g. recombinant human serum albumin).
To prepare the flow cell priming mix with BSA, combine Flow Cell Flush (FCF) and Flow Cell Tether (FCT), as directed below. Mix by pipetting at room temperature.
Note: We are in the process of reformatting our kits with single-use tubes into a bottle format. Please follow the instructions for your kit format.
Single-use tubes format: Add 5 µl Bovine Serum Albumin (BSA) at 50 mg/ml and 30 µl Flow Cell Tether (FCT) directly to a tube of Flow Cell Flush (FCF).
Bottle format: In a suitable tube for the number of flow cells, combine the following reagents:
| Reagent | Volume per flow cell |
|---|---|
| Flow Cell Flush (FCF) | 1,170 µl |
| Bovine Serum Albumin (BSA) at 50 mg/ml | 5 µl |
| Flow Cell Tether (FCT) | 30 µl |
| Total volume | 1,205 µl |
Open the MinION or GridION device lid and slide the flow cell under the clip. Press down firmly on the flow cell to ensure correct thermal and electrical contact.
OPTIONAL ACTION
Complete a flow cell check to assess the number of pores available before loading the library.
This step can be omitted if the flow cell has been checked previously.
See the flow cell check instructions in the MinKNOW protocol for more information.
Slide the flow cell priming port cover clockwise to open the priming port.
IMPORTANT
Take care when drawing back buffer from the flow cell. Do not remove more than 20-30 µl, and make sure that the array of pores are covered by buffer at all times. Introducing air bubbles into the array can irreversibly damage pores.
After opening the priming port, check for a small air bubble under the cover. Draw back a small volume to remove any bubbles:
- Set a P1000 pipette to 200 µl
- Insert the tip into the priming port
- Turn the wheel until the dial shows 220-230 µl, to draw back 20-30 µl, or until you can see a small volume of buffer entering the pipette tip
__Note:__ Visually check that there is continuous buffer from the priming port across the sensor array.
Load 800 µl of the priming mix into the flow cell via the priming port, avoiding the introduction of air bubbles. Wait for five minutes. During this time, prepare the library for loading by following the steps below.
Thoroughly mix the contents of the Library Beads (LIB) by pipetting.
IMPORTANT
The Library Beads (LIB) tube contains a suspension of beads. These beads settle very quickly. It is vital that they are mixed immediately before use.
We recommend using the Library Beads (LIB) for most sequencing experiments. However, the Library Solution (LIS) is available for more viscous libraries.
In a new 1.5 ml Eppendorf DNA LoBind tube, prepare the library for loading as follows:
| Reagent | Volume per flow cell |
|---|---|
| Sequencing Buffer (SB) | 37.5 µl |
| Library Beads (LIB) mixed immediately before use, or Library Solution (LIS), if using | 25.5 µl |
| DNA library | 12 µl |
| Total | 75 µl |
Complete the flow cell priming:
- Gently lift the SpotON sample port cover to make the SpotON sample port accessible.
- Load 200 µl of the priming mix into the flow cell priming port (not the SpotON sample port), avoiding the introduction of air bubbles.
Mix the prepared library gently by pipetting up and down just prior to loading.
Add 75 μl of the prepared library to the flow cell via the SpotON sample port in a dropwise fashion. Ensure each drop flows into the port before adding the next.
Gently replace the SpotON sample port cover, making sure the bung enters the SpotON port and close the priming port.
IMPORTANT
Install the light shield on your flow cell as soon as library has been loaded for optimal sequencing output.
We recommend leaving the light shield on the flow cell when library is loaded, including during any washing and reloading steps. The shield can be removed when the library has been removed from the flow cell.
Place the light shield onto the flow cell, as follows:
Carefully place the leading edge of the light shield against the clip. Note: Do not force the light shield underneath the clip.
Gently lower the light shield onto the flow cell. The light shield should sit around the SpotON cover, covering the entire top section of the flow cell.
CAUTION
The MinION Flow Cell Light Shield is not secured to the flow cell and careful handling is required after installation.
END OF STEP
Close the device lid and set up a sequencing run on MinKNOW.
7. Data acquisition and basecalling
How to start sequencing
Once you have loaded your flow cell, the sequencing run can be started on MinKNOW, our sequencing software that controls the device, data acquisition and real-time basecalling. For more detailed information on setting up and using MinKNOW, please see the MinKNOW protocol.
MinKNOW can be used and set up to sequence in multiple ways:
- On a computer either directly or remotely connected to a sequencing device.
- Directly on a GridION, MinION Mk1C or PromethION 24/48 sequencing device.
For more information on using MinKNOW on a sequencing device, please see the device user manuals:
To start a sequencing run on MinKNOW:
1. Navigate to the start page and click Start sequencing.
2. Fill in your experiment details, such as name and flow cell position and sample ID.
3. Select the sequencing kit used in the library preparation on the Kit page.
4. Configure the sequencing and output parameters for your sequencing run or keep to the default settings on the Run configuration tab.
Note: If basecalling was turned off when a sequencing run was set up, basecalling can be performed post-run on MinKNOW. For more information, please see the MinKNOW protocol.
5. Click Start on the Review page to start the sequencing run.
Data analysis after sequencing
After sequencing has completed on MinKNOW, the flow cell can be reused or returned, as outlined in the Flow cell reuse and returns section.
After sequencing and basecalling, the data can be analysed. For further information about options for basecalling and post-basecalling analysis, please refer to the Data Analysis document.
In the Downstream analysis section, we outline further options for analysing your data.
8. Flow cell reuse and returns
Materials
- Flow Cell Wash Kit (EXP-WSH004)
After your sequencing experiment is complete, if you would like to reuse the flow cell, please follow the Flow Cell Wash Kit protocol and store the washed flow cell at 2-8°C.
The Flow Cell Wash Kit protocol is available on the Nanopore Community.
TIP
We recommend you to wash the flow cell as soon as possible after you stop the run. However, if this is not possible, leave the flow cell on the device and wash it the next day.
Alternatively, follow the returns procedure to flush out the flow cell ready to send back to Oxford Nanopore.
Instructions for returning flow cells can be found here.
Note: All flow cells must be flushed with deionised water before returning the product.
IMPORTANT
If you encounter issues or have questions about your sequencing experiment, please refer to the Troubleshooting Guide that can be found in the online version of this protocol.
9. Downstream analysis
Post-basecalling analysis
There are several options for further analysing your basecalled data:
1. EPI2ME workflows
For in-depth data analysis, Oxford Nanopore Technologies offers a range of bioinformatics tutorials and workflows available in EPI2ME. The platform provides a vehicle where workflows deposited in GitHub by our Research and Applications teams can be showcased with descriptive texts, functional bioinformatics code and example data.
2. Research analysis tools
Oxford Nanopore Technologies' Research division has created a number of analysis tools, which are available in the Oxford Nanopore GitHub repository. The tools are aimed at advanced users, and contain instructions for how to install and run the software. They are provided as-is, with minimal support.
3. Community-developed analysis tools
If a data analysis method for your research question is not provided in any of the resources above, please refer to the Bioinformatics section of the Resource centre. Numerous members of the Nanopore Community have developed their own tools and pipelines for analysing nanopore sequencing data, most of which are available on GitHub. Please be aware that these tools are not supported by Oxford Nanopore Technologies, and are not guaranteed to be compatible with the latest chemistry/software configuration.
10. Issues during DNA/RNA extraction and library preparation
Below is a list of the most commonly encountered issues, with some suggested causes and solutions.
We also have an FAQ section available on the Nanopore Community Support section.
If you have tried our suggested solutions and the issue still persists, please contact Technical Support via email (support@nanoporetech.com) or via LiveChat in the Nanopore Community.
Low sample quality
| Observation | Possible cause | Comments and actions |
|---|---|---|
| Low DNA purity (Nanodrop reading for DNA OD 260/280 is <1.8 and OD 260/230 is <2.0–2.2) | The DNA extraction method does not provide the required purity | The effects of contaminants are shown in the Contaminants document. Please try an alternative extraction method that does not result in contaminant carryover. Consider performing an additional SPRI clean-up step. |
| Low RNA integrity (RNA integrity number <9.5 RIN, or the rRNA band is shown as a smear on the gel) | The RNA degraded during extraction | Try a different RNA extraction method. For more info on RIN, please see the RNA Integrity Number document. Further information can be found in the DNA/RNA Handling page. |
| RNA has a shorter than expected fragment length | The RNA degraded during extraction | Try a different RNA extraction method. For more info on RIN, please see the RNA Integrity Number document. Further information can be found in the DNA/RNA Handling page. We recommend working in an RNase-free environment, and to keep your lab equipment RNase-free when working with RNA. |
Low DNA recovery after AMPure bead clean-up
| Observation | Possible cause | Comments and actions |
|---|---|---|
| Low recovery | DNA loss due to a lower than intended AMPure beads-to-sample ratio | 1. AMPure beads settle quickly, so ensure they are well resuspended before adding them to the sample. 2. When the AMPure beads-to-sample ratio is lower than 0.4:1, DNA fragments of any size will be lost during the clean-up. |
| Low recovery | DNA fragments are shorter than expected | The lower the AMPure beads-to-sample ratio, the more stringent the selection against short fragments. Please always determine the input DNA length on an agarose gel (or other gel electrophoresis methods) and then calculate the appropriate amount of AMPure beads to use.  |
| Low recovery after end-prep | The wash step used ethanol <70% | DNA will be eluted from the beads when using ethanol <70%. Make sure to use the correct percentage. |
11. Issues during the sequencing run
Below is a list of the most commonly encountered issues, with some suggested causes and solutions.
We also have an FAQ section available on the Nanopore Community Support section.
If you have tried our suggested solutions and the issue still persists, please contact Technical Support via email (support@nanoporetech.com) or via LiveChat in the Nanopore Community.
Fewer pores at the start of sequencing than after Flow Cell Check
| Observation | Possible cause | Comments and actions |
|---|---|---|
| MinKNOW reported a lower number of pores at the start of sequencing than the number reported by the Flow Cell Check | An air bubble was introduced into the nanopore array | After the Flow Cell Check it is essential to remove any air bubbles near the priming port before priming the flow cell. If not removed, the air bubble can travel to the nanopore array and irreversibly damage the nanopores that have been exposed to air. The best practice to prevent this from happening is demonstrated in this video. |
| MinKNOW reported a lower number of pores at the start of sequencing than the number reported by the Flow Cell Check | The flow cell is not correctly inserted into the device | Stop the sequencing run, remove the flow cell from the sequencing device and insert it again, checking that the flow cell is firmly seated in the device and that it has reached the target temperature. If applicable, try a different position on the device (GridION/PromethION). |
| MinKNOW reported a lower number of pores at the start of sequencing than the number reported by the Flow Cell Check | Contaminations in the library damaged or blocked the pores | The pore count during the Flow Cell Check is performed using the QC DNA molecules present in the flow cell storage buffer. At the start of sequencing, the library itself is used to estimate the number of active pores. Because of this, variability of about 10% in the number of pores is expected. A significantly lower pore count reported at the start of sequencing can be due to contaminants in the library that have damaged the membranes or blocked the pores. Alternative DNA/RNA extraction or purification methods may be needed to improve the purity of the input material. The effects of contaminants are shown in the Contaminants Know-how piece. Please try an alternative extraction method that does not result in contaminant carryover. |
MinKNOW script failed
| Observation | Possible cause | Comments and actions |
|---|---|---|
| MinKNOW shows "Script failed" | Restart the computer and then restart MinKNOW. If the issue persists, please collect the MinKNOW log files and contact Technical Support. If you do not have another sequencing device available, we recommend storing the flow cell and the loaded library at 4°C and contact Technical Support for further storage guidance. |
Pore occupancy below 40%
| Observation | Possible cause | Comments and actions |
|---|---|---|
| Pore occupancy <40% | Not enough library was loaded on the flow cell | Ensure you load the recommended amount of good quality library in the relevant library prep protocol onto your flow cell. Please quantify the library before loading and calculate mols using tools like the Promega Biomath Calculator, choosing "dsDNA: µg to pmol" |
| Pore occupancy close to 0 | The Ligation Sequencing Kit was used, and sequencing adapters did not ligate to the DNA | Make sure to use the NEBNext Quick Ligation Module (E6056) and Oxford Nanopore Technologies Ligation Buffer (LNB, provided in the sequencing kit) at the sequencing adapter ligation step, and use the correct amount of each reagent. A Lambda control library can be prepared to test the integrity of the third-party reagents. |
| Pore occupancy close to 0 | The Ligation Sequencing Kit was used, and ethanol was used instead of LFB or SFB at the wash step after sequencing adapter ligation | Ethanol can denature the motor protein on the sequencing adapters. Make sure the LFB or SFB buffer was used after ligation of sequencing adapters. |
| Pore occupancy close to 0 | No tether on the flow cell | Tethers are adding during flow cell priming (FLT/FCT tube). Make sure FLT/FCT was added to FB/FCF before priming. |
Shorter than expected read length
| Observation | Possible cause | Comments and actions |
|---|---|---|
| Shorter than expected read length | Unwanted fragmentation of DNA sample | Read length reflects input DNA fragment length. Input DNA can be fragmented during extraction and library prep. 1. Please review the Extraction Methods in the Nanopore Community for best practice for extraction. 2. Visualise the input DNA fragment length distribution on an agarose gel before proceeding to the library prep.  In the image above, Sample 1 is of high molecular weight, whereas Sample 2 has been fragmented.3. During library prep, avoid pipetting and vortexing when mixing reagents. Flicking or inverting the tube is sufficient. |
Large proportion of unavailable pores
| Observation | Possible cause | Comments and actions |
|---|---|---|
Large proportion of unavailable pores (shown as blue in the channels panel and pore activity plot)  The pore activity plot above shows an increasing proportion of "unavailable" pores over time. | Contaminants are present in the sample | Some contaminants can be cleared from the pores by the unblocking function built into MinKNOW. If this is successful, the pore status will change to "sequencing pore". If the portion of unavailable pores stays large or increases: 1. A nuclease flush using the Flow Cell Wash Kit (EXP-WSH004) can be performed, or 2. Run several cycles of PCR to try and dilute any contaminants that may be causing problems. |
Large proportion of inactive pores
| Observation | Possible cause | Comments and actions |
|---|---|---|
| Large proportion of inactive/unavailable pores (shown as light blue in the channels panel and pore activity plot. Pores or membranes are irreversibly damaged) | Air bubbles have been introduced into the flow cell | Air bubbles introduced through flow cell priming and library loading can irreversibly damage the pores. Watch the Priming and loading your flow cell video for best practice |
| Large proportion of inactive/unavailable pores | Certain compounds co-purified with DNA | Known compounds, include polysaccharides, typically associate with plant genomic DNA. 1. Please refer to the Plant leaf DNA extraction method. 2. Clean-up using the QIAGEN PowerClean Pro kit. 3. Perform a whole genome amplification with the original gDNA sample using the QIAGEN REPLI-g kit. |
| Large proportion of inactive/unavailable pores | Contaminants are present in the sample | The effects of contaminants are shown in the Contaminants Know-how piece. Please try an alternative extraction method that does not result in contaminant carryover. |
Reduction in sequencing speed and q-score later into the run
| Observation | Possible cause | Comments and actions |
|---|---|---|
| Reduction in sequencing speed and q-score later into the run | For Kit 9 chemistry (e.g. SQK-LSK109), fast fuel consumption is typically seen when the flow cell is overloaded with library (please see the appropriate protocol for your DNA library to see the recommendation). | Add more fuel to the flow cell by following the instructions in the MinKNOW protocol. In future experiments, load lower amounts of library to the flow cell. |
Temperature fluctuation
| Observation | Possible cause | Comments and actions |
|---|---|---|
| Temperature fluctuation | The flow cell has lost contact with the device | Check that there is a heat pad covering the metal plate on the back of the flow cell. Re-insert the flow cell and press it down to make sure the connector pins are firmly in contact with the device. If the problem persists, please contact Technical Services. |
Failed to reach target temperature
| Observation | Possible cause | Comments and actions |
|---|---|---|
| MinKNOW shows "Failed to reach target temperature" | The instrument was placed in a location that is colder than normal room temperature, or a location with poor ventilation (which leads to the flow cells overheating) | MinKNOW has a default timeframe for the flow cell to reach the target temperature. Once the timeframe is exceeded, an error message will appear and the sequencing experiment will continue. However, sequencing at an incorrect temperature may lead to a decrease in throughput and lower q-scores. Please adjust the location of the sequencing device to ensure that it is placed at room temperature with good ventilation, then re-start the process in MinKNOW. Please refer to this FAQ for more information on MinION Mk 1B temperature control. |
Guppy – no input .fast5 was found or basecalled
| Observation | Possible cause | Comments and actions |
|---|---|---|
| No input .fast5 was found or basecalled | input_path did not point to the .fast5 file location | The --input_path has to be followed by the full file path to the .fast5 files to be basecalled, and the location has to be accessible either locally or remotely through SSH. |
| No input .fast5 was found or basecalled | The .fast5 files were in a subfolder at the input_path location | To allow Guppy to look into subfolders, add the --recursive flag to the command |
Guppy – no Pass or Fail folders were generated after basecalling
| Observation | Possible cause | Comments and actions |
|---|---|---|
| No Pass or Fail folders were generated after basecalling | The --qscore_filtering flag was not included in the command | The --qscore_filtering flag enables filtering of reads into Pass and Fail folders inside the output folder, based on their strand q-score. When performing live basecalling in MinKNOW, a q-score of 7 (corresponding to a basecall accuracy of ~80%) is used to separate reads into Pass and Fail folders. |
Guppy – unusually slow processing on a GPU computer
| Observation | Possible cause | Comments and actions |
|---|---|---|
| Unusually slow processing on a GPU computer | The --device flag wasn't included in the command | The --device flag specifies a GPU device to use for accelerate basecalling. If not included in the command, GPU will not be used. GPUs are counted from zero. An example is --device cuda:0 cuda:1, when 2 GPUs are specified to use by the Guppy command. |
Last updated: 8/21/2024
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