Oct 10, 2024

Public workspaceMycelium RNA Extraction and Library Prep

  • Chidrupi Golla1
  • 1North Carolina State University
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Protocol CitationChidrupi Golla 2024. Mycelium RNA Extraction and Library Prep. protocols.io https://dx.doi.org/10.17504/protocols.io.n2bvjn7ppgk5/v1
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
Protocol status: Other
I drafted this protocol
Created: October 03, 2024
Last Modified: October 10, 2024
Protocol Integer ID: 109139
Abstract
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.
Attachments
Materials
General Equipment and Consumables
  • centrifuge
  • timer
  • Glass beakers
  • 50 mL conical tubes
  • centrifuge tubes
  • 3mL Eppendorf tube
  • Deionized water
  • Qubit and Nanodrop fluorometers
  • P1000 pipette and tips
  • P200 pipette and tips
  • P100 pipette and tips
  • P20 pipette and tips
  • P10 pipette and tips
  • P2 pipette and tips
  • Ice bucket with ice
  • Timer

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)
  • RNaseOUT, 40 U/μl (Life Technologies, cat # 10777019)
  • RNase Cocktail Enzyme Mix (ThermoFisher, cat # AM2286)
  • Bovine Serum Albumin (BSA) (50 mg/ml) (e.g Invitrogen UltraPure BSA 50 mg/ml, AM2616)

Equipment
  • Magnetic rack, suitable for 1.5 ml Eppendorf tubes
  • Microfuge
  • Vortex mixer
  • Thermal cycler
  • Pre-chilled freezer block at -20° C for 200 µl tubes 
  • Hula mixer
Protocol materials
ReagentMaxima H Minus Reverse TranscriptaseThermo Fisher ScientificCatalog ##EP0741
In 2 steps
ReagentTRIzol ReagentThermo Fisher ScientificCatalog #15596026
Step 20
ReagentRNaseOUT™ Recombinant Ribonuclease InhibitorThermo Fisher ScientificCatalog #10777019
In 2 steps
Before start
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
Obtaining Mycelium Samples: Extraction of soil fungal mycelium
9m
9m
Sieve collected soil samples through a 2-mm sieve to remove any root fragments
Disperse a Amount5 g soil sample into Amount100 mL of deionized water

Stir the mixture at 500 rpm using a magnetic stirrer for Duration00:05:00

5m
Filter the mixture through a 1000 µm pore nylon mesh
Thorough wash the oversized particles with Amount100 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 Amount35 mL of deionized water for storage if needed (store at 4℃)

Centrifuge the samples for Duration00:03:00 at 31000xg

3m
Discard the supernatant
Disperse the pellet by adding Amount50 mL of 45.5% sucrose solution and hand-shaking vigorously

Centrifuge the solution at Centrifigation50 x g for Duration00:01:00

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 Temperature20-30 °C if needed.

RNA extraction
RNA extraction
Ground the particles into a fine powder in liquid nitrogen
Add Amount2 mL of ReagentTRIzol 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 Duration00:05:00

5m
Add Amount300 µL of chloroform and sahe the tube vigorously for 15 seconds

Incubate at room temperature for Duration00:03:00

3m
Centrifuge the samples at Centrifigation13.000 x g for Duration00:15:00 at Temperature4 °C

15m
Repeat steps 5-7
Precipitate the RNA using Amount500 µL of isopropanol at Temperature-20 °C for Duration02:00:00

2h
Collect the precipitated RNA through centrifugation at Centrifigation13000 x g for Duration00:15:00 at Temperature4 °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
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.


Reagent1. Thaw at room Temperature2. Briefly spin down3. Mix well by pipetting
User-supplied VN Primer diluted to 2 µM
User-supplied Strand-Switching Primer diluted to 10 µM
10 mM dNTP solution
RNaseOUTNot frozen
Maxima H Minus Reverse TranscriptaseNot frozen
Maxima H Minus 5x RT BufferMix by vortexing

ReagentRNaseOUT™ Recombinant Ribonuclease InhibitorThermo Fisher ScientificCatalog #10777019
ReagentMaxima H Minus Reverse TranscriptaseThermo Fisher ScientificCatalog ##EP0741

Prepare the RNA in nuclease-free water.
Add Amount1 µg of total RNA to a 0.2 ml PCR tube

Adjust the volume to Amount7.5 µL with nuclease-free water

Mix the tube by flicking
Spin down in a microfuge
Prepare the following reaction in the 0.2 ml PCR tube containing the prepared RNA input:

ReagentVolume
RNA input from previous step7.5 µl
VN Primer diluted to 2 µM2.5 µl
10 mM dNTPS1 µl
Total Volume11 µl

Mix gently by flicking the tube and then spin down
Incubate at Temperature60 °C for Duration00:05:00 and then snap cool on a pre-chilled freezer block for Duration00:01:00 .

6m
In a separate tube, mix the following together:
5x RT Buffer4 µl
RNaseOUT1 µl
Nuclease-Free water1 µl
Strand-Switching Primer diluted to 10 uM2 µl
Total Volume8 µl
ReagentRNaseOUT™ Recombinant Ribonuclease InhibitorThermo Fisher ScientificCatalog #10777019

Mix gently by flicking the tube, and spin down.
Add the Amount8 µL of strand-switching reagents (prepared in steps 6-7) to the Amount11 µL of snap-cooled mRNA (from steps 2-5). Mix by flicking the tube and spin down.

Incubate at Temperature42 °C for Duration00:02:00 in the thermal cycler.

2m
Add 1 µl of ReagentMaxima H Minus Reverse TranscriptaseThermo Fisher ScientificCatalog ##EP0741 . The total volume is now Amount20 µL .

Mix gently by flicking the tube, and spin down.
Incubate using the following protocol using a thermal cycler:

Cycle StepTemperatureTime No. of cycles
Reverse Transcription and Strand-Switching42 ℃90 minutes1
Heat inactivation85 ℃5 minutes1
Hold4 ℃


Library Preparation: RNA Degradation and Second strand synthesis
Library Preparation: RNA Degradation and Second strand synthesis
  1. Thaw the following reagents and spin down briefly using a microfuge, before mixing as indicated in the table below, and place on ice.

Reagent1. Thaw at room Temperature2. Briefly spin down3. Mix well by pipetting
User-supplied PR2 Primer diluted to 10 µM
RNaes Cocktail Enzyme MixNot 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 Amount1 µL RNase Cocktail Enzyme Mix (ThermoFisher, cat # AM2286) to the reverse transcription reaction.

Incubate the reaction for Duration00:10:00 at Temperature37 °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 Amount17 µL of resuspended AMPure XP beads (AXP) to the reaction and mix by flicking the tube.

Amount0 µL Incubate on a Hula mixer (rotator mixer) for Duration00:05:00 at room temperature.

5m
Prepare Amount500 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 Amount200 µL of 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 ~Duration00:00:30 , but do not dry the pellet to the point of cracking.

30s
Remove the tube from the magnetic rack and resuspend pellet in Amount20 µL nuclease-free water.

Incubate on a Hula mixer (rotator mixer) for Duration00:10:00 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 Duration00:01:00 .

1m
Remove and retain Amount20 µL of eluate into a clean 1.5 ml Eppendorf DNA LoBind tube.

Prepare the following reaction in a 0.2 ml thin-walled PCR tube:


ReagentVolume
2x LongAmp Taq Master Mix 25 µl
PR2 Primer diluted to 10 μM2 µl
Reverse-transcribed sample from above20 µl
Nuclease-free water3 µl
Total Volume50 µl

Incubate using the following protocol:


Cycle StepTemperatureTime No. of cycles
Denaturation94 ℃1 minute1
Annealing50 ℃1 minute1
Extension65 ℃15 minutes1
Hold4 ℃

Resuspend the AMPure XP beads (AXP) by vortexing.
Transfer the sample to a clean 1.5 ml Eppendorf DNA LoBind tube.
Add Amount40 µL of resuspended AMPure XP beads (AXP) to the reaction and mix by flicking the tube.

Incubate on a Hula mixer (rotator mixer) for Duration00:05:00 at room temperature.

5m
Prepare Amount500 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 Amount200 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 ~Duration00:00:30 , but do not dry the pellet to the point of cracking.

30s
Remove the tube from the magnetic rack and resuspend pellet in Amount21 µL nuclease-free water.

Incubate on a Hula mixer (rotator mixer) for Duration00:10:00 at room temperature.

10m
Amount0 µL Briefly spin down the tube and pellet the beads on the magnet until the eluate is clear and colorless, for at least Duration00:01:00 .

1m
Remove and retain Amount21 µL of 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
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.
  1. Combine the following reagents in a 0.2 ml PCR tube:


ReagentVolume
cDNA sample25 µl
Nuclease-free water30 µl
Ultra II End-prep reaction buffer7 µl
Ultra II End-prep enzyme mix3 µl
Total Volume60 µl

Thoroughly mix the reaction by gently pipetting and briefly spinning down.
Using a thermal cycler, incubate at Temperature20 °C for Duration00:05:00 and Temperature65 °C for Duration00:05:00 .

10m
Resuspend the AMPure XP Beads (AXP) by vortexing.
Transfer the DNA sample to a clean 1.5 ml Eppendorf DNA LoBind tube.
Add Amount60 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 Duration00:05:00 at room temperature.

5m
Prepare Amount500 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 Amount200 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 ~Duration00:00:30 , but do not dry the pellet to the point of cracking.

30s
Remove the tube from the magnetic rack and resuspend pellet in Amount61 µL nuclease-free water. Incubate for Duration00:02:00 at room temperature.

2m
Pellet the beads on a magnet until the eluate is clear and colorless, for at least Duration00:01:00

1m
Remove and retain Amount61 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 Temperature20 °C for Duration00:05:00 and Temperature65 °C for Duration00:05:00 .

10m
Resuspend the AMPure XP Beads (AXP) by vortexing.
Transfer the DNA sample to a clean 1.5 ml Eppendorf DNA LoBind tube.
Add Amount60 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 Duration00:05:00 at room temperature.

5m
Prepare Amount500 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 Amount200 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 ~Duration00:00:30 , but do not dry the pellet to the point of cracking.

30s
Remove the tube from the magnetic rack and resuspend pellet in Amount61 µL nuclease-free water. Incubate for Duration00:02:00 at room temperature.

2m
Pellet the beads on a magnet until the eluate is clear and colorless, for at least Duration00:01:00 .

1m
Remove and retain Amount61 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 Temperature20 °C for Duration00:05:00 and Temperature65 °C for Duration00:05:00 .

10m
Resuspend the AMPure XP Beads (AXP) by vortexing.
Transfer the DNA sample to a clean 1.5 ml Eppendorf DNA LoBind tube.
Add Amount60 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 Duration00:05:00 at room temperature.

5m
Prepare Amount500 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 Amount200 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 Duration00:00:30 , but do not dry the pellet to the point of cracking.

30s
Remove the tube from the magnetic rack and resuspend pellet in Amount61 µL nuclease-free water. Incubate for Duration00:02:00 at room temperature.

2m
Pellet the beads on a magnet until the eluate is clear and colorless, for at least Duration00:01:00 .

1m
Remove and retain Amount61 µL of eluate into a clean 1.5 ml Eppendorf DNA LoBind tube.

Library Preparation: Adapter ligation and clean-up
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
ReagentVolume
cDNA sample from the previous step60 µl
Ligation Adapter (LA)5 µl
Ligation Buffer (LNB)25 µl
NEBNext Quick T4 DNA Ligase10 µl
Total100 µl


Thoroughly mix the reaction by gently pipetting and briefly spinning down.
Incubate the reaction for Duration00:10:00 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 Duration00:05:00 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 Amount250 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 ~Duration00:00:30 , but do not dry the pellet to the point of cracking.

30s
Remove the tube from the magnetic rack and resuspend the pellet in Amount15 µL Elution Buffer (EB). Spin down and incubate forDuration00:10:00 at room temperature.

10m
Pellet the beads on a magnet until the eluate is clear and colorless, for at least Duration00:01:00 .

1m
Remove and retain Amount15 µL of eluate containing the DNA library into a clean 1.5 ml Eppendorf DNA LoBind tube.

Quantify Amount1 µL of the eluted sample using a Qubit fluorometer

Depending on your DNA library fragment size, prepare your final library in Amount12 µL of Elution Buffer (EB).


Fragment library lengthFlow 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
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.
  1. 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.


ReagentVolume per flow cell
Flow Cell Flush (FCF)1,170 µl
Bovine Serum Albumin (BSA) at 50 mg/ml5 µl
Flow Cell Tether (FCT)30 µl
Total volume1,205 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 Amount200 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 Amount800 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:


ReagentVolume per flow cell
Sequencing Buffer (SB)37.5 µl
Library Beads (LIB) mixed immediately before use, or Library Solution (LIS), if using25.5 µl
DNA library12 µl
Total75 µl

Complete the flow cell priming:
Gently lift the SpotON sample port cover to make the SpotON sample port accessible.
LoadAmount200 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.