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: Working
We use this protocol and it's working
Created: July 18, 2023
Last Modified: July 19, 2023
Protocol Integer ID: 85191
Keywords: extraction, gDNA, MinION, nematode, library preparation, uHMW gDNA, ONT
Abstract
This custom protocol optimizes extraction, purification, and Oxford Nanopore Technologies (ONT) MinION library preparation for ultra-high molecular weight genomic DNA (uHMW gDNA) from parasitic nematodes. It can be used effectively with both low-input samples (e.g., a single adult hookworm) and high-input samples (e.g., a chunk of tissue from an Ascaris sp. adult).
Zymo DNA Elution BufferZymo ResearchCatalog #D3004-4-10
Step 51
Quick T4 DNA LigaseNew England BiolabsCatalog #E7180S
In 2 steps
NEB Monarch PestleNEBCatalog #T3002-1
Step 4
Before start
For new kits, add 1,040 µL Zymo Proteinase K Storage Buffer to each tube of Zymo Proteinase K (20 mg) prior to use. The final concentration of Proteinase K is ~20 mg/ml. Store resuspended Proteinase K at -20°C after mixing.
Part 1: Ultra-HWM gDNA extraction | Zymo Quick-DNA HWM MagBead Plus Kit | ~3 hr
Part 1: Ultra-HWM gDNA extraction | Zymo Quick-DNA HWM MagBead Plus Kit | ~3 hr
Set dry bath to 55 °C
For each sample, add the following to a clean 1.5 mL microcentrifuge tube to create a master mix:
95 µLZymo DNA Elution BufferZymo ResearchCatalog #D3004-4-1
Vortex the master mix gently to mix, then spin down and keep on ice
Using a new pipette tip or sterilized forceps, add one whole worm (or a piece of tissue) directly from tissue preservative to the bottom of a clean 1.5 mL microcentrifuge tube
Use a new NEB Monarch PestleNEBCatalog #T3002-1 to grind and crush the tissue in the tube. Keep the pestle in the tube
Add 200 µL master mix (prepared in Part 1 Step 2) to each tube containing tissue and pestle
Continue using the pestle to grind the tissue within the master mix until homogenized. Remove the pestle, being careful to keep any tissue in the tube by wiping the pestle on the tube edges as it is removed
Close the tube and mix by inverting and flicking gently, then spin down briefly to recollect tissue and liquids
Incubate sample in dry bath at 55 °C for 02:30:00 to Overnight until tissue solubilizes. During incubation, flick tube every 00:20:00 to agitate tissues, then briefly spin down to recollect liquids and replace tube in dry bath
3h 10m
Part 2: Ultra-HWM gDNA purification | Zymo Quick-DNA HWM MagBead Plus Kit | ~4 hr + overnight incubation
Part 2: Ultra-HWM gDNA purification | Zymo Quick-DNA HWM MagBead Plus Kit | ~4 hr + overnight incubation
2h 20m
2h 20m
Set dry bath to 37 °C
Add 400 µLZymo Quick-DNA™ MagBinding Buffer Zymo ResearchCatalog #D4077-1-150 to each sample
Flick tubes to mix, then spin down briefly to recollect liquids
Add 33 µLZymo MagBinding BeadsZymo ResearchCatalog #D4100-2-6 to each sample
To ensure DNA binds to beads, mix on a rotator mixer at a low speed for 02:00:00 at Room temperature. Spin down briefly before proceeding with the next step
2h
Set sample tubes on a magnetic stand until beads have separated from solution, then remove and discard the supernatant. Remove sample tubes from the magnetic stand.
Add 500 µLZymo Quick-DNA™ MagBinding Buffer Zymo ResearchCatalog #D4077-1-150 to each sample
Flick to mix initially, then mix on a rotator mixer at a low speed for 00:20:00 at Room temperature. Spin down briefly before proceeding with the next step
20m
Set sample tubes on a magnetic stand until beads have separated from the solution, then remove and discard the supernatant. Remove sample tubes from the magnetic stand
Add 500 µLZymo DNA Pre-Wash BufferZymo ResearchCatalog #D3004-5-250 to each sample
Flick to mix, then spin down briefly
Set sample tubes on a magnetic stand until beads have separated from solution, then remove and discard the supernatant. Remove sample tubes from the magnetic stand
Add 900 µLZymo g-DNA Wash BufferZymo ResearchCatalog #D3004-2-200 to each sample
Flick to mix, then spin down briefly
Transfer the entire sample (all liquid and beads) to a new clean 1.5 mL microcentrifuge tube
Set samples (now in new tubes) on a magnetic stand until beads have separated from the solution, then remove and discard the supernatant. Remove sample tubes from the magnetic stand
Add 900 µLZymo g-DNA Wash BufferZymo ResearchCatalog #D3004-2-200 to each sample
Flick to mix, then spin down briefly
Transfer the entire sample (all liquid and beads) to a new clean 1.5 mL microcentrifuge tube
Set samples (now in new tubes) on a magnetic stand until beads have separated from the solution, then remove and discard the supernatant. Leave sample tubes on the magnetic stand
Use a P10 pipette to remove any residual liquid from the bottom of the tube
Air dry the beads for up to 00:20:00 and proceed to next step once beads are dry, but not over-dry
20m
Add 50 µLZymo DNA Elution BufferZymo ResearchCatalog #D3004-4-50 to each sample and flick gently several times to mix. Spin down briefly
Incubate in dry bath at 37 °C for 02:00:00. During incubation, flick tube every 00:20:00 to agitate tissues, then briefly spin down to recollect liquids and replace tube in dry bath
2h 20m
Incubate on bench top at Room temperature overnight.
After overnight incubation, set tubes on a magnetic stand until beads have separated from solution, then move the supernatant (now containing eluted gDNA) to a new clean 1.5 mL microcentrifuge tube
Re-suspend beads in 20 µLof Nuclease-free Water in case there is no (or not enough) gDNA in final elution
Use 1 µL of final elution to quantify extraction via Qubit analysis
Use 1 µL of final elution to assess fragment size distribution via TapeStation
Part 3: DNA repair and end-prep | Zymo Clean & Concentrator, ONT Ligation Sequencing, & NEBNext Companion Kits | ~1.5 hr
Part 3: DNA repair and end-prep | Zymo Clean & Concentrator, ONT Ligation Sequencing, & NEBNext Companion Kits | ~1.5 hr
1h
1h
Set dry bath to 65 °C
Defrost the needed NEB DNA and End Repair reagents on ice (see Part 3 Step 38)
For each sample, add the following to a clean 0.2 mL PCR tube to create a master mix, pipetting 10–20 times between each addition to mix:
3.5 µLNEBNext® FFPE DNA Repair BufferNew England BiolabsCatalog #E7180S
2 µLNEBNext FFPE DNA Repair Mix - 96 rxnsNew England BiolabsCatalog #M6630L
3.5 µLNEBNext Ultra II End Prep Reaction BufferNew England BiolabsCatalog #E7647
3 µLNEBNext Ultra II End Prep Enzyme MixNew England BiolabsCatalog #E7646
Keep master mix on ice
Add 12 µL of master mix (prepared in Part 3 Step 38) from the PCR tube directly into each 1.5 mL microcentrifuge tube containing extracted & purified uHWM gDNA (from Part 2). Mix all components by gently flicking, and spin tubes down to recollect liquids
Incubate samples at Room temperature for 00:10:00
10m
Incubate samples in dry bath at 65 °C for 00:10:00
10m
Add 4 volumes of Zymo DNA MagBinding BufferZymo ResearchCatalog #D4012-1-50 to each sample and mix well by flicking and inverting
Spin samples down briefly and add 20 µLZymo MagBinding BeadsZymo ResearchCatalog #D4100-5-2
Mix samples on rotating mixer at a low speed at Room temperature for 01:30:00
1h 30m
Briefly spin down samples and pellet on a magnetic stand (1–2 min) until the supernatant is clear and colorless. With the tubes still on the magnet, pipette off and discard the supernatant
Add 500 µLZymo DNA Wash BufferZymo ResearchCatalog #D4003-2-24 and then remove from magnetic stand, and mix well by flicking and inverting
Briefly spin samples down briefly and transfer to magnetic stand to allow beads to pellet until solution is clear (1–2 min). With the tubes still on the magnet, pipette off and discard the supernatant
Add 500 µLZymo DNA Wash BufferZymo ResearchCatalog #D4003-2-24 and then remove from magnetic stand, and mix well by flicking and inverting
Briefly spin samples down briefly and transfer to magnetic stand to allow beads to pellet until solution is clear (1–2 min). With the tubes still on the magnet, pipette off and discard the supernatant
Air dry the beads for 00:10:00
10m
Add 52 µLZymo DNA Elution BufferZymo ResearchCatalog #D3004-4-10
Manually agitate samples for 00:10:00 to 00:20:00 by gently flicking/inverting (and occasionally spinning dow to recollect liquids)
30m
Briefly spin samples down and pellet the beads on a magnet until the eluate is clear and colorless (1–2 min)
Remove and retain the 52 µL of eluate (containing repaired & end-prepped DNA) to a new clean 1.5 mL microcentrifuge tube
Use 1 µL of final elution to quantify via Qubit assay
Use 1 µL of final elution to assess fragment size distribution via TapeStation
Part 4: Adaptor ligation and clean up | ONT Ligation Sequencing & NEBNext Companion Kits | ~3 hr + overnight incubation
Part 4: Adaptor ligation and clean up | ONT Ligation Sequencing & NEBNext Companion Kits | ~3 hr + overnight incubation
1h
1h
Set dry bath to 37 °C
Remove AMPure XP BeadsBeckman CoulterCatalog #A63880 from storage at 4 °C and allow them to come to Room temperature
Spin down Ligation Adaptor (LA)Oxford Nanopore Technologies andQuick T4 DNA LigaseNew England BiolabsCatalog #E7180S and place on ice
Thaw ONT Ligation Buffer (LNB)Oxford Nanopore Technologies at Room temperature, spin down, and mix by pipetting. Place on ice immediately after thawing and mixing
Thaw Elution Buffer (EB)Oxford Nanopore Technologies at Room temperature, vortex to mix, spin down, and place on ice
Thaw one tube each of Short Fragment Buffer (SFB)Oxford Nanopore Technologies and Long Fragment Buffer (LFB)Oxford Nanopore Technologies at Room temperature, vortex to mix, spin down, and place on ice
For each sample, add the following, in order, to a new clean 1.5 mL microcentrifuge tube, pipetting 10–20 times between each addition to mix:
For each sample, prepare 1:3 SFB:LFB titrated wash mix by adding the following to a new clean 1.5 mL microcentrifuge tube, and then vortex to mix:
125 µLShort Fragment Buffer (SFB)Oxford Nanopore Technologies
375 µLLong Fragment Buffer (LFB)Oxford Nanopore Technologies
Keep titrated wash mix on ice after vortexing
Pipette 40 µL of master mix (prepared in Part 4 Step 62) directly into entire volume of repaired and end-prepped gDNA from Part 3. Mix all components by gently flicking and spin tube down to recollect liquids
Incubate the reaction 00:15:00 at Room temperature
15m
Resuspend AMPure XP BeadsBeckman CoulterCatalog #A63880 by vortexing and add 0.4X volume resuspended beads to each sample, then flick to mix
Mix on a rotator mixer at a low speed for 01:00:00 at Room temperature
1h
Spin down the sample and pellet on a magnetic stand. Keeping the tube on the stand, pipette off and discard the supernatant
Wash the beads by adding 250 µL 1:3 SFB:LFB titrated wash mix (prepared in Part 4 Step 63). Flick the beads to resuspend, spin down, then return to the magnetic rack and allow the beads to pellet. Remove the supernatant using a pipette and discard
Wash the beads by adding 250 µL 1:3 SFB:LFB titrated wash mix (prepared in Part 4 Step 63). Flick the beads to resuspend, spin down, then return to the magnetic rack and allow the beads to pellet. Remove the supernatant using a pipette and discard
Spin down the beads and place them back on the magnetic rack. Use a P10 pipette to pipette of any residual liquid and allow beads to air-dry for 00:00:30 to 00:02:00
2m 30s
Remove the tube from the magnetic stand and resuspend the beads in 15 µLElution Buffer (EB)Oxford Nanopore Technologies
Briefly spin down and incubate in dry bath at 37 °C for 02:00:00. During incubation, flick tube every 00:20:00 to agitate tissues, then briefly spin down to recollect liquids and replace tube in dry bath
2h 20m
Incubate on the bench top at Room temperature overnight
After overnight incubation, pellet the beads on a magnet until the eluate is clear and colorless (at least 1 min)
Remove and retain the 15 µL of eluate (containing the prepared library) to a new clean 1.5 mL microcentrifuge tube
Use 1 µL of final elution to quantify library via Qubit analysis