TITLE: Express Protocol NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®) (NEB #E7650S/L) without PCR Bead Cleanup
AUTHORS: Isabel Gautreau

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details methods for the NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®), NEB #E7650S/L 24/96 reactions, express protocol. </div><br/><div class = "text-block"><span>This protocol </span><span style = "font-weight:bold;">does not include a cleanup step for each sample after cDNA synthesis and ligation</span><span>. Performing the cleanup step creates libraries with higher yields and less likelihood for adaptor dimer. Skipping these steps reduces hands on time, but may require an extra cleanup at the end of library prep of the pooled sample and we have added an extra PCR cycle. </span></div></div>

[STEPS]
?. [cDNA Synthesis]
Gently mix and spin down the LunaScript RT SuperMix reagent. Prepare the cDNA synthesis reaction as described below:COMPONENT VOLUMERNA Sample8 µl(lilac) LunaScript RT SuperMix2 µlTotal Volume10 µlFor no template controls, mix the following components:COMPONENTVOLUME(white) Nuclease-free Water8 µl(lilac) LunaScript RT SuperMix2 µlTotal Volume10 µl
COMPONENT VOLUMERNA Sample8 µl(lilac) LunaScript RT SuperMix2 µlTotal Volume10 µl
COMPONENTVOLUME(white) Nuclease-free Water8 µl(lilac) LunaScript RT SuperMix2 µlTotal Volume10 µl
?. [cDNA Synthesis]
Incubate reactions in a thermocycler* with the following steps:CYCLE STEPTEMPTIMECYCLESPrimer Annealing25°C2 minutes1cDNA Synthesis55°C20 minutesHeat Inactivation95°C1 minuteHold4°C∞
CYCLE STEPTEMPTIMECYCLESPrimer Annealing25°C2 minutes1cDNA Synthesis55°C20 minutesHeat Inactivation95°C1 minuteHold4°C∞
Samples can be stored at   for up to a week.
?. [Targeted cDNA Amplification]
4.5 µl cDNA input is recommended. If using less than 4.5 µl of cDNA, add nuclease-free water to a final volume of 4.5 µl. We recommend setting up the cDNA synthesis and cDNA amplification reactions in different rooms to minimize cross-contamination of future reactions.Use of the NEBNext ARTIC Human Primer Mix 1 and 2 are optional. If used, the appropriate NEBNext ARTIC Human Primer Mix and NEBNext ARTIC SARS-CoV-2 Primer Mix should be combined prior to use. More specifically, NEBNext ARTIC Human Primer Mix 1 should be combined with NEBNext ARTIC SARS-CoV-2 Primer Mix 1 and NEBNext ARTIC Human Primer Mix 2 with NEBNext ARTIC SARS-CoV-2 Primer Mix 2. Mixing directions are listed below.
?. [Targeted cDNA Amplification]
Gently mix and spin down reagents. Prepare the split pool cDNA amplification reactions as described below:For Pool Set A: If using the NEBNext ARTIC Human Primer Mix and a 24 reaction kit, combine  with  in a new tube, vortex and spin down reagents. If using a 96 reaction kit, combine  with  in a new tube, vortex and spin down reagents. Use  for each Pool Set A reaction.COMPONENT VOLUMEcDNA (Step 2)4.5 µl(lilac) Q5 Hot Start High-Fidelity 2X Master Mix6.25 µlNEBNext ARTIC SARS-Cov-2 Primer Mix 1 * 1.75 µlTotal Volume 12.5 µlFor Pool Set B:If using the NEBNext ARTIC Human Primer Mix and a 24 reaction kit, combine  with  in a new tube, vortex and spin down reagents. If using a 96 reaction kit, combine  with  in a new tube, vortex and spin down reagents. Use  for each Pool Set B reaction.COMPONENT VOLUMEcDNA (Step 2)4.5 µl(lilac) Q5 Hot Start High-Fidelity 2X Master Mix6.25 µlNEBNext ARTIC SARS-CoV-2 Primer Mix 2* 1.75 µlTotal Volume12.5 µl
[NEBNext ARTIC Human Primer Mix 1]
[NEBNext ARTIC SARS-CoV-2 Primer Mix 1]
[NEBNext ARTIC Primer Mix 1]
[NEBNext ARTIC SARS-CoV-2 Primer Mix 1]
[of the combined mix]
COMPONENT VOLUMEcDNA (Step 2)4.5 µl(lilac) Q5 Hot Start High-Fidelity 2X Master Mix6.25 µlNEBNext ARTIC SARS-Cov-2 Primer Mix 1 * 1.75 µlTotal Volume 12.5 µl
[NEBNext ARTIC Human Primer Mix 2]
[NEBNext ARTIC SARS-CoV-2 Primer Mix 2]
[NEBNext ARTIC Human Primer Mix 2]
[NEBNext ARTIC SARS-CoV-2 Primer Mix 2]
[ of the combined mix]
COMPONENT VOLUMEcDNA (Step 2)4.5 µl(lilac) Q5 Hot Start High-Fidelity 2X Master Mix6.25 µlNEBNext ARTIC SARS-CoV-2 Primer Mix 2* 1.75 µlTotal Volume12.5 µl
?. [Targeted cDNA Amplification]
Incubate reactions in a thermocycler* with the following steps:CYCLE STEPTEMPTIMECYCLESInitial Denaturation98°C30 seconds1Denature95°C15 seconds35Annealing/Extension63°C5 minutesHold4°C∞1
CYCLE STEPTEMPTIMECYCLESInitial Denaturation98°C30 seconds1Denature95°C15 seconds35Annealing/Extension63°C5 minutesHold4°C∞1
?. [Targeted cDNA Amplification]
Combine the Pool A and Pool B PCR reactions for each sample.
Samples can be stored at   for up to a week.
?. [Pooling of cDNA Amplicons.]
Transfer 2.5 µl of the pooled cDNA amplicons to a fresh tube.
Note: When cleanup of the pooled cDNA amplicons is skipped, the amplicons must be diluted prior to library prep.
?. [Pooling of cDNA Amplicons.]
Add 22.5 µl of low TE for a final volume of 25 µl.
To confirm the size of the 400 bp amplicons, pooled cDNA amplicons can be run on a TapeStation® without cleanup. To run on a TapeStation, dilute an aliquot of the pooled amplicons 10-fold with 0.1X TE Buffer and run 2 μl on a DNA High Sensitivity ScreenTape. (See Figure 8. below for example of amplicon size profile on a TapeStation).
?. [NEBNext End Prep]
Add the following components to a sterile nuclease-free tube:COMPONENTVOLUME(green) NEBNext Ultra II End Prep Enzyme Mix1.5 µl(green) NEBNext Ultra II End Prep Reaction Buffer3.5 µlTargeted cDNA Amplicons (Step 8)25 µlTotal Volume30 µl
COMPONENTVOLUME(green) NEBNext Ultra II End Prep Enzyme Mix1.5 µl(green) NEBNext Ultra II End Prep Reaction Buffer3.5 µlTargeted cDNA Amplicons (Step 8)25 µlTotal Volume30 µl
?. [NEBNext End Prep]
Set a 100 µl or 200 µl pipette to 25 µl and then pipette the entire volume up and down at least 10 times to mix thoroughly. Perform a quick spin to collect all liquid from the sides of the tube.
It is important to mix well. The presence of a small amount of bubbles will not interfere with performance
?. [NEBNext End Prep]
Place in a thermocycler* and run the following program:TEMPTIME20°C30 minutes65°C30 minutes4°C∞
TEMPTIME20°C30 minutes65°C30 minutes4°C∞
If necessary, samples can be stored at  ; however, a slight loss in yield (~20%) may be observed. We recommend continuing with adaptor ligation before stopping.
?. [Adaptor Ligation]
Add the following components directly to the End Prep Reaction Mixture:COMPONENT VOLUMEEnd Prep Reaction Mixture (previous step) 30 µl(red) NEBNext Adaptor for Illumina** 1.25 µl(red) NEBNext Ultra II Ligation Master Mix* 15 µlTotal Volume46.25 µl
COMPONENT VOLUMEEnd Prep Reaction Mixture (previous step) 30 µl(red) NEBNext Adaptor for Illumina** 1.25 µl(red) NEBNext Ultra II Ligation Master Mix* 15 µlTotal Volume46.25 µl
Do not premix adaptor with the Ligation Master Mix.
?. [Adaptor Ligation]
Set a 100 µl or 200 µl pipette to 40 µl and then pipette the entire volume up and down at least 10 times to mix thoroughly. Perform a quick spin to collect all liquid from the sides of the tube.
Caution: The NEBNext Ultra II Ligation Master Mix is very viscous. Care should be taken to ensure adequate mixing of the ligation reaction, as incomplete mixing will result in reduced ligation efficiency. The presence of a small amount of bubbles will not interfere with performance.
?. [Adaptor Ligation]
Incubate at  for  in a thermocycler with the heated lid off.
20 °C
?. [Adaptor Ligation]
Add  to the ligation mixture from the previous step.
[(red or blue) USER® Enzyme]
Steps 15 and 16 are only required for use with non- indexed NEBNext Adaptors. USER enzyme can be found in the NEBNext Multiplex Oligos (www.neb.com/oligos).
?. [Adaptor Ligation]
Mix well and incubate at  for  with the heated lid set to ≥ .
37 °C
47 °C
Samples can be stored overnight at  .Only a portion of the ligation reaction (7.5 µl) will move forward to PCR enrichment.
?. [PCR Enrichment of Adaptor-ligated DNA]
Follow step-case A. if you are using the following oligos:Use option A for any NEBNext Oligo kit where index primers are supplied in tubes. These kits have the forward and reverse primers supplied in separate tubes. Primers are supplied at 10 µM (each).Follow step-case B. if you are using the following oligos :Use Option B for any NEBNext Oligo kit where index primers are supplied in a 96-well plate format. These kits have the forward and reverse (i7 and i5) primers combined. Primers are supplied at 10 µM (combined).
?. [PCR Enrichment of Adaptor-ligated DNA]
Add the following components to a sterile strip tube:COMPONENTVOLUMEAdaptor Ligated DNA Fragments (Step 16)7.5 μl(blue) NEBNext Library PCR Master Mix12.5 μlUniversal PCR Primer/i5 Primer *,**2.5 μlIndex (X) Primer/i7 Primer *,**2.5 μlTotal Volume25 μl
COMPONENTVOLUMEAdaptor Ligated DNA Fragments (Step 16)7.5 μl(blue) NEBNext Library PCR Master Mix12.5 μlUniversal PCR Primer/i5 Primer *,**2.5 μlIndex (X) Primer/i7 Primer *,**2.5 μlTotal Volume25 μl
?. [PCR Enrichment of Adaptor-ligated DNA]
Set a 100 μl pipette to 20 μl and then pipette the entire volume up and down at least 10 times to mix thoroughly. Perform a quick spin to collect all liquid from the sides of the tube.
?. [PCR Enrichment of Adaptor-ligated DNA]
Place the tube on a thermocycler8 and perform PCR amplification using the following PCR cycling conditions:CYCLE STEPTEMPTIMECYCLESInitial Denaturation98°C30 seconds1Denaturation98°C10 seconds6**Annealing/Extension65°C75 secondsFinal Extension65°C5 minutes1Hold4°C∞
CYCLE STEPTEMPTIMECYCLESInitial Denaturation98°C30 seconds1Denaturation98°C10 seconds6**Annealing/Extension65°C75 secondsFinal Extension65°C5 minutes1Hold4°C∞
?. [Cleanup of PCR Reaction]
The amount of NEBNext Sample Purification Beads provided here are for use with the sample contained in the exact buffer at this step. These volumes may not work properly for a cleanup at a different step in the workflow. For cleanups of samples contained in different buffer conditions, the volumes may need to be experimentally determined.
?. [Cleanup of PCR Reaction]
Vortex NEBNext Sample Purification Beads to resuspend.
?. [Cleanup of PCR Reaction]
Add  to the PCR reaction. Mix well by pipetting up and down at least 10 times. Be careful to expel all of the liquid out of the tip during the last mix. Vortexing for 3-5 seconds on high can also be used. If centrifuging samples after mixing, be sure to stop the centrifugation before the beads start to settle out.
[(0.7X) resuspended beads]
?. [Cleanup of PCR Reaction]
Incubate samples on bench top for at least  at .
0 Room temperature
?. [Cleanup of PCR Reaction]
Place the tube/plate on an appropriate magnetic stand to separate the beads from the supernatant. If necessary, quickly spin the sample to collect the liquid from the sides of the tube or plate wells before placing on the magnetic stand.
?. [Cleanup of PCR Reaction]
After 5 minutes (or when the solution is clear), carefully remove and discard the supernatant. Be careful not to disturb the beads that contain DNA targets.
Caution: do not discard the beads.
?. [Cleanup of PCR Reaction]
Add  to the tube/plate while in the magnetic stand. Incubate at  for , and then carefully remove and discard the supernatant. Be careful not to disturb the beads that contain DNA targets.
[80% freshly prepared ethanol]
0 Room temperature
?. [Cleanup of PCR Reaction]
Repeat the previous step once for a total of two washes:Add  to the tube/plate while in the magnetic stand. Incubate at  for , and then carefully remove and discard the supernatant. Be careful not to disturb the beads that contain DNA targets.Be sure to remove all visible liquid after the second wash. If necessary, briefly spin the tube/plate, place back on the magnet and remove traces of ethanol with a p10 pipette tip.
[80% freshly prepared ethanol]
0 Room temperature
?. [Cleanup of PCR Reaction]
Air dry the beads for up to 5 minutes while the tube/plate is on the magnetic stand with the lid open.
Caution: Do not over-dry the beads. This may result in lower recovery of DNA. Elute the samples when the beads are still dark brown and glossy looking, but when all visible liquid has evaporated. When the beads turn lighter brown and start to crack, they are too dry.
?. [Cleanup of PCR Reaction]
Remove the tube/plate from the magnetic stand. Elute the DNA target from the beads by adding .
[0.1X TE]
?. [Cleanup of PCR Reaction]
Mix well by pipetting up and down 10 times, or on a vortex mixer. Incubate for at least  at . If necessary, quickly spin the sample to collect the liquid from the sides of the tube or plate wells before placing back on the magnetic stand.
0 Room temperature
?. [Cleanup of PCR Reaction]
Place the tube/plate on the magnetic stand. After 5 minutes (or when the solution is clear), transfer  to a new PCR tube and store at .
15 µl
-20 °C
?. [Cleanup of PCR Reaction]
Assess the library size distribution on an Agilent Bioanalyzer or TapeStation. The sample may need to be diluted before loading. A peak size of ~520 bp is expected (Figure 33).
Samples can be stored at –20°C.
If excess adaptor dimer peak is observed at 150-180 bp, a second 0.7X bead cleanup can be performed. The second 0.7X cleanup will result in slightly larger libraries which will not affect sequencing results.
?. [PCR Enrichment of Adaptor-ligated DNA]
Add the following components to a sterile strip tube:COMPONENTVOLUMEAdaptor Ligated DNA Fragments (Step 16)7.5 μl(blue) NEBNext Library PCR Master Mix12.5 μlIndex Primer Mix *5 μlTotal Volume25 μl
COMPONENTVOLUMEAdaptor Ligated DNA Fragments (Step 16)7.5 μl(blue) NEBNext Library PCR Master Mix12.5 μlIndex Primer Mix *5 μlTotal Volume25 μl
?. [PCR Enrichment of Adaptor-ligated DNA]
Set a 100 μl pipette to 20 μl and then pipette the entire volume up and down at least 10 times to mix thoroughly. Perform a quick spin to collect all liquid from the sides of the tube.
?. [PCR Enrichment of Adaptor-ligated DNA]
Place the tube on a thermocycler and perform PCR amplification using the following PCR cycling conditions:CYCLE STEPTEMPTIMECYCLESInitial Denaturation98°C30 seconds1Denaturation98°C10 seconds5*Annealing/Extension65°C75 secondsFinal Extension65°C5 minutes1Hold4°C∞
CYCLE STEPTEMPTIMECYCLESInitial Denaturation98°C30 seconds1Denaturation98°C10 seconds5*Annealing/Extension65°C75 secondsFinal Extension65°C5 minutes1Hold4°C∞
?. [PCR Enrichment of Adaptor-ligated DNA]
Proceed to Cleanup of PCR Amplification in the next section.
?. [Cleanup of PCR Reaction]
The NEBNext Sample Purification Beads provided here are for use with the sample contained in the exact buffer at this step. These volumes may not work properly for a cleanup at a different step in the workflow. For cleanups of samples contained in different buffer conditions, the volumes may need to be experimentally determined.
?. [Cleanup of PCR Reaction]
Vortex NEBNext Sample Purification Beads to resuspend.
?. [Cleanup of PCR Reaction]
Add  to the PCR reaction. Mix well by pipetting up and down at least 10 times. Be careful to expel all of the liquid out of the tip during the last mix. Vortexing for 3-5 seconds on high can also be used. If centrifuging samples after mixing, be sure to stop the centrifugation before the beads start to settle out.
[(0.9X) resuspended beads]
?. [Cleanup of PCR Reaction]
Incubate samples on bench top for at least  at .
0 Room temperature
?. [Cleanup of PCR Reaction]
Place the tube/plate on an appropriate magnetic stand to separate the beads from the supernatant. If necessary, quickly spin the sample to collect the liquid from the sides of the tube or plate wells before placing on the magnetic stand.
?. [Cleanup of PCR Reaction]
After 5 minutes (or when the solution is clear), carefully remove and discard the supernatant. Be careful not to disturb the beads that contain DNA targets.
Caution: do not discard the beads.
?. [Cleanup of PCR Reaction]
Add  to the tube/plate while in the magnetic stand. Incubate at  for , and then carefully remove and discard the supernatant. Be careful not to disturb the beads that contain DNA targets.
[80% freshly prepared ethanol]
0 Room temperature
?. [Cleanup of PCR Reaction]
Repeat the previous step once for a total of two washes:Add  to the tube/plate while in the magnetic stand. Incubate at  for , and then carefully remove and discard the supernatant. Be careful not to disturb the beads that contain DNA targets.Be sure to remove all visible liquid after the second wash. If necessary, briefly spin the tube/plate, place back on the magnet and remove traces of ethanol with a p10 pipette tip.
[80% freshly prepared ethanol]
0 Room temperature
?. [Cleanup of PCR Reaction]
Air dry the beads for up to 5 minutes while the tube/plate is on the magnetic stand with the lid open.
Caution: Do not over-dry the beads. This may result in lower recovery of DNA. Elute the samples when the beads are still dark brown and glossy looking, but when all visible liquid has evaporated. When the beads turn lighter brown and start to crack, they are too dry.
?. [Cleanup of PCR Reaction]
Remove the tube/plate from the magnetic stand. Elute the DNA target from the beads by adding .
[0.1X TE]
?. [Cleanup of PCR Reaction]
Mix well by pipetting up and down 10 times, or on a vortex mixer. Incubate for at least  at . If necessary, quickly spin the sample to collect the liquid from the sides of the tube or plate wells before placing back on the magnetic stand.
0 Room temperature
?. [Cleanup of PCR Reaction]
Place the tube/plate on the magnetic stand. After 5 minutes (or when the solution is clear), transfer  to a new PCR tube and store at .
15 µl
-20 °C
?. [Cleanup of PCR Reaction]
Check the size distribution on an Agilent Bioanalyzer or TapeStation. The sample may need to be diluted before loading. A peak size of ~520 bp is expected (Figure 61).
Samples can be stored at  .