License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
The goal of the Mycelium RNA extraction and sequencing protocol is to sequence mycelium RNA. The protocol begins with a method to extract mycelium from soil samples. Following this process, the mycelium can be stored if needed. The next step is to extract the RNA from the mycelium samples. The RNA collected will be prepared for sequencing using a MinION flow cell. The library preparation and sample loading follows the Ligation sequencing kit for cDNA by Oxford Nanopore Technologies. The RNA is reverse transcribed into cDNA and the cDNA is then sequenced.
The Ligation sequencing kit for cDNA does include third-party items that need to be purchased from outside sources.
Some key considerations for this protocol are to maintain the sterility of the sample and to prevent fungal rot. The fungal samples may have other organic materials like wood chips or plant roots. The extraction procedure should prevent contamination from occurring by filtering out large particles. Fungal rot can be prevented by maintaining a temperature range between 20°C to 30°C.
Obtaining Mycelium Samples: Extraction of soil fungal mycelium protocol materials
Equipment
sieve
magnetic stirrer
1000 µm pore nylon mesh
50 µm pore metal sleeve
50 µm pore nylon mesh
Consumables
45.5% sucrose solution
RNA extraction protocol
Consumables
TRIzol Reagent from Invitrogen
chloroform
isopropanol
Ligation sequencing V14 - Direct cDNA sequencing kit materials
User-supplied VN Primer, 2 µM
User-supplied Strand-Switching Primer, 10 µM
User-supplied PR2 Primer, 10 µM
NEBNext Companion Module for Oxford Nanopore Technologies Ligation Sequencing (NEB, E7180S, or E7180L). Alternatively, you can use the NEBNext products below:
NEBNext Ultra II End Repair / dA-tailing Module (NEB, E7546)
NEBNext Quick Ligation Module (NEB, E6056)
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
10 mM dNTP solution (e.g. NEB N0447)
LongAmp Taq 2X Master Mix(e.g. NEB M0287)
Maxima H Minus Reverse Transcriptase (200 U/µl) with 5x RT Buffer (ThermoFisher, cat # EP0751)
This kit contains reagents from a third-party site and not included in the Ligation sequencing V14 - Direct cDNA sequencing kit by Oxford Nanopore Technologies.
Obtaining Mycelium Samples: Extraction of soil fungal mycelium
9m
Sieve collected soil samples through a 2-mm sieve to remove any root fragments
Disperse a 5 g soil sample into 100 mL of deionized water
Stir the mixture at 500 rpm using a magnetic stirrer for 00:05:00
5m
Filter the mixture through a 1000 µm pore nylon mesh
Thorough wash the oversized particles with 100 mL of deionized water
Repeat steps 4-5 with the filtrate
Filter the filtrate twice through a 50 µm pore metal sleeve containing a 50 µm pore nylon mesh
Discard the filtrate and collect the oversized particles in a 50 mL tube by rinsing them using 35 mLof deionized water for storage if needed (store at 4℃)
Centrifuge the samples for 00:03:00 at 31000xg
3m
Discard the supernatant
Disperse the pellet by adding 50 mLof 45.5% sucrose solution and hand-shaking vigorously
Centrifuge the solution at 50 x g for 00:01:00
1m
Filter the supernatant through a three-layered 50 µm pore size nylon mesh
Repeat steps 9-13 four more times
Discard the remaining soil pellet
Thoroughly wash the particles collected on the nylon mesh with deionized water. Make sure to rinse out the sucrose solution
Collect the particles into a 3 mL Eppendorf tube and allow them to dry completely
Store between 20-30 °Cif needed.
RNA extraction
Ground the particles into a fine powder in liquid nitrogen
Add 2 mL of TRIzol ReagentThermo Fisher ScientificCatalog #15596026 and ground the sample further until the slurry is thawed
Split the sample into two 2 mL Eppendorf tubes
Incubate at room temperature for 00:05:00
5m
Add 300 µL of chloroform and sahe the tube vigorously for 15 seconds
Incubate at room temperature for 00:03:00
3m
Centrifuge the samples at 13.000 x g for 00:15:00at 4 °C
15m
Repeat steps 5-7
Precipitate the RNA using 500 µL of isopropanol at -20 °Cfor 02:00:00
2h
Collect the precipitated RNA through centrifugation at 13000 x g for 00:15:00 at 4 °C
15m
Discard the supernatant and resuspend the RNA pellets
Quantify the RNA using the Qubit and Nanodrop fluorometers
Library Preparation: Reverse transcription and strand-switching
Thaw the following reagents and spin down briefly using a microfuge, before mixing as indicated in the table below, and place on ice.
Reagent
1. Thaw at room Temperature
2. Briefly spin down
3. Mix well by pipetting
User-supplied VN Primer diluted to 2 µM
✓
✓
✓
User-supplied Strand-Switching Primer diluted to 10 µM
Add the 8 µL of strand-switching reagents (prepared in steps 6-7) to the 11 µL of snap-cooled mRNA (from steps 2-5). Mix by flicking the tube and spin down.
Incubate at 42 °C for 00:02:00 in the thermal cycler.
2m
Add 1 µl of Maxima H Minus Reverse TranscriptaseThermo Fisher ScientificCatalog ##EP0741. The total volume is now 20 µL.
Mix gently by flicking the tube, and spin down.
Incubate using the following protocol using a thermal cycler:
Cycle Step
Temperature
Time
No. of cycles
Reverse Transcription and Strand-Switching
42 ℃
90 minutes
1
Heat inactivation
85 ℃
5 minutes
1
Hold
4 ℃
∞
Library Preparation: RNA Degradation and Second strand synthesis
Thaw the following reagents and spin down briefly using a microfuge, before mixing as indicated in the table below, and place on ice.
Reagent
1. Thaw at room Temperature
2. Briefly spin down
3. Mix well by pipetting
User-supplied PR2 Primer diluted to 10 µM
✓
✓
✓
RNaes Cocktail Enzyme Mix
Not frozen
✓
✓
LongAmp Taq 2X Master Mix
✓
✓
✓
Thaw the AMPure XP Beads (AXP) at room temperature and mix by vortexing. Keep the beads at room temperature.
Add 1 µL RNase Cocktail Enzyme Mix (ThermoFisher, cat # AM2286) to the reverse transcription reaction.
Incubate the reaction for 00:10:00 at 37 °C in a thermal cycler.
10m
Resuspend the AMPure XP beads (AXP) by vortexing.
Transfer the sample to a clean 1.5 ml Eppendorf DNA LoBind tube.
Add 17 µL of resuspended AMPure XP beads (AXP) to the reaction and mix by flicking the tube.
0 µL Incubate on a Hula mixer (rotator mixer) for 00:05:00 at room temperature.
5m
Prepare 500 µL of fresh 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.
Keep the tubes on the magnet and wash the beads with 200 µLof freshly prepared 80% ethanol without disturbing the pellet. Remove the ethanol using a pipette and discard.
Note
Note: If the pellet was disturbed, wait for beads to pellet again before removing the ethanol.
Repeat the previous step.
Spin down and place the tube back on the magnet. Pipette off any residual ethanol. Allow to dry for ~00:00:30, but do not dry the pellet to the point of cracking.
30s
Remove the tube from the magnetic rack and resuspend pellet in 20 µL nuclease-free water.
Incubate on a Hula mixer (rotator mixer) for 00:10:00 at room temperature.
10m
Briefly spin down the tube and pellet the beads on the magnet until the eluate is clear and colorless, for at least 00:01:00.
1m
Remove and retain 20 µLof eluate into a clean 1.5 ml Eppendorf DNA LoBind tube.
Prepare the following reaction in a 0.2 ml thin-walled PCR tube:
Reagent
Volume
2x LongAmp Taq Master Mix
25 µl
PR2 Primer diluted to 10 μM
2 µl
Reverse-transcribed sample from above
20 µl
Nuclease-free water
3 µl
Total Volume
50 µl
Incubate using the following protocol:
Cycle Step
Temperature
Time
No. of cycles
Denaturation
94 ℃
1 minute
1
Annealing
50 ℃
1 minute
1
Extension
65 ℃
15 minutes
1
Hold
4 ℃
∞
Resuspend the AMPure XP beads (AXP) by vortexing.
Transfer the sample to a clean 1.5 ml Eppendorf DNA LoBind tube.
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 00:05:00at room temperature.
5m
Prepare 500 µL of fresh 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.
Keep the tubes 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.
Note
If the pellet was disturbed, wait for the beads to pellet again before removing the ethanol.
Repeat the previous step.
Spin down and place the tube back on the magnet. Pipette off any residual ethanol. Allow to dry for ~00:00:30, but do not dry the pellet to the point of cracking.
30s
Remove the tube from the magnetic rack and resuspend pellet in 21 µL nuclease-free water.
Incubate on a Hula mixer (rotator mixer) for 00:10:00 at room temperature.
10m
0 µL Briefly spin down the tube and pellet the beads on the magnet until the eluate is clear and colorless, for at least 00:01:00.
1m
Remove and retain 21 µLof eluate into a clean 1.5 ml Eppendorf DNA LoBind tube.
Quantify the DNA using a Agilent Bioanalyzer and Qubit Fluorometer
Library Preparation: cDNA repair and end-prep
Prepare the NEBNext Ultra II End Repair / dA-tailing Module reagents in accordance with manufacturer's instructions, and place on ice.
Combine the following reagents in a 0.2 ml PCR tube:
Reagent
Volume
cDNA sample
25 µl
Nuclease-free water
30 µl
Ultra II End-prep reaction buffer
7 µl
Ultra II End-prep enzyme mix
3 µl
Total Volume
60 µl
Thoroughly mix the reaction by gently pipetting and briefly spinning down.
Using a thermal cycler, incubate at 20 °C for 00:05:00 and 65 °C for 00:05:00.
10m
Resuspend the AMPure XP Beads (AXP) by vortexing.
Transfer the DNA sample to a clean 1.5 ml Eppendorf DNA LoBind tube.
Add 60 µLof 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 00:05:00 at room temperature.
5m
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 ~00:00:30, but do not dry the pellet to the point of cracking.
30s
Remove the tube from the magnetic rack and resuspend pellet in 61 µL nuclease-free water. Incubate for 00:02:00 at room temperature.
2m
Pellet the beads on a magnet until the eluate is clear and colorless, for at least 00:01:00
1m
Remove and retain 61 µL of eluate into a clean 1.5 ml Eppendorf DNA LoBind tube.
Thoroughly mix the reaction by gently pipetting and briefly spinning down.
Using a thermal cycler, incubate at 20 °C for 00:05:00 and 65 °C for 00:05:00.
10m
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 00:05:00 at room temperature.
5m
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 µLof 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 ~00:00:30, but do not dry the pellet to the point of cracking.
30s
Remove the tube from the magnetic rack and resuspend pellet in 61 µLnuclease-free water. Incubate for 00:02:00at room temperature.
2m
Pellet the beads on a magnet until the eluate is clear and colorless, for at least 00:01:00.
1m
Remove and retain 61 µL of eluate into a clean 1.5 ml Eppendorf DNA LoBind tube.
Thoroughly mix the reaction by gently pipetting and briefly spinning down.
Using a thermal cycler, incubate at 20 °C for 00:05:00 and 65 °C for 00:05:00.
10m
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 00:05:00 at room temperature.
5m
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 colorless. 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 00:00:30 , but do not dry the pellet to the point of cracking.
30s
Remove the tube from the magnetic rack and resuspend pellet in 61 µL nuclease-free water. Incubate for 00:02:00 at room temperature.
2m
Pellet the beads on a magnet until the eluate is clear and colorless, for at least 00:01:00.
1m
Remove and retain 61 µLof eluate into a clean 1.5 ml Eppendorf DNA LoBind tube.
Library Preparation: Adapter ligation and clean-up
Spin down the Ligation Adapter (LA) and Quick T4 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
cDNA sample from the previous step
60 µl
Ligation Adapter (LA)
5 µl
Ligation Buffer (LNB)
25 µl
NEBNext Quick T4 DNA Ligase
10 µl
Total
100 µl
Thoroughly mix the reaction by gently pipetting and briefly spinning down.
Incubate the reaction for 00:10:00 at room temperature.
10m
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 00:05:00 at room temperature.
5m
Spin down the sample and pellet on a magnet. Keep the tube on the magnet, and pipette off the supernatant when clear and colorless.
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 ~00:00:30, but do not dry the pellet to the point of cracking.
30s
Remove the tube from the magnetic rack and resuspend the pellet in 15 µLElution Buffer (EB). Spin down and incubate for00:10:00at room temperature.
10m
Pellet the beads on a magnet until the eluate is clear and colorless, for at least 00:01:00.
1m
Remove and retain 15 µL of eluate containing the DNA library into a clean 1.5 ml Eppendorf DNA LoBind tube.
Quantify 1 µL of the 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
Loading and priming MinION
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.
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.
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
BSA is not required but improves sequencing
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.
Slide the flow cell priming port cover clockwise to open the priming port.
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
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.
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.
Load200 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.
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.
Close the device lid and set up a sequencing run on MinKNOW
Protocol references
1. Awad A, Pena R. 2023. An improved method for extraction of soil fungal mycelium. MethodsX 11:102477.
2. Schumann U, Smith NA, Wang M-B. 2013. A fast and efficient method for preparation of high-quality RNA from fungal mycelia. BMC Res Notes 6:71.
3. 2023. Ligation sequencing V14 - Direct cDNA sequencing (SQK-LSK114) (DCS_9187_v114_revI_31Jul2024). Oxf Nanopore Technol. https://nanoporetech.com/document/ligation-sequencing-v14-direct-cdna-sequencing. Retrieved 21 September 2024.