TaME-seq2: Tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling. Alexander Hesselberg Løvestad, Milan S. Stosic, Jean-Marc Costanzi, Irene Kraus Christiansen, Hege Vangstein Aamot, Ole Herman Ambur, Trine B. Rounge Virol J20, 44 (2023). https://doi.org/10.1186/s12985-023-02002-5
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
Tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling (TaME-seq2). Viral genome and integration enrichment library preparation protocol.
Manuscript:
TaME-seq2: Tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling.
Alexander Hesselberg Løvestad, Milan S. Stosic, Jean-Marc Costanzi, Irene Kraus Christiansen, Hege Vangstein Aamot, Ole Herman Ambur, Trine B. Rounge medRxiv 2022.12.22.22283851
Prepare samples consisting of extracted DNA or reverse transcribed cDNA.
The method consists of three main parts:
Part 1:
Tagmentation of samples using the Illumina DNA Prep kit.
Part 2:
Multiplex PCR reaction of tagmented DNA/cDNA, using virus-specific primers and i5/i7 indexes.
Part 3:
Clean-up and size selection using purification beads/Ampure XP beads.
Materials
A
B
C
Component
Supplier
Catalog number
Illumina® DNA Prep, (M) Tagmentation (96 Samples)
Illumina
20018705
QIAGEN Multiplex PCR Kit (100)
Quiagen
206143
AMPure XP 60 mL
Beckman Coulter
A63881
Sample preparation
Sample preparation
Prepare and normalize DNA/cDNA samples by measuring sample concentration and diluting in nuclease-free water if necessary.
Sample volume should be 15 µL
50 ng input is recommended, but the protocol works with less and performance is more dependent on viral load.
Tagmentation
Tagmentation
Prepare a master mix for the tagmentation reaction and add sample DNA and master mix to individual wells.
A
B
C
Reagent
1x
10x
Bead linked transposoms (BLT)
5 μL
50 μL
Tagmentation buffer 1 (TB1)
5 μL
50 μL
Sample DNA/cDNA
15 μL
Total
25 μL
10x10 μL
Tagmentation reagent mix table
Incubate the samples as follows:
00:15:00 at 55 °C
Hold at 4 °C
15m
Add 5 µL of Tagmentation stop buffer (TSB) to each sample.
Incubate sample for 00:15:00 at 37 °C
15m
Wash the samples
Place tubes on the magnetic rack for 00:03:00 (or until solution is clear)
Discard supernatant
Remove tube from magnetic rack and add 50 µL Tagment wash buffer (TWB) and mix to resuspend beads
Place tubes on magnetic rack for 00:03:00 and remove supernatant
Repeat step 3 and 4 for a total of 2 washes
Add 50 µL TWB to samples and mix
Close cap on tubes and place on magnet. Allow to incubate for at least 00:03:00 and continue the protocol. The samples will be used later in the PCR
9m
Amplification of tagmented DNA
Amplification of tagmented DNA
Make the PCR master mix
A
B
C
Reagent
1x
10x
2x PCR master mix
12,5 μl
125 μl
Q-solution x5
2,5 μl
25 μl
Primer pool (15 μM)
1 μl
i5/i7 indexes (10 μM)
2 μl
Nuclease-free water
7 μl
70 μl
Total
25 μl
22 μL x 10 μL + 3 μL primers per sample
2. Remove supernatant from samples prepared in step 6.7 and remove from magnetic rack
3. Add 30 µL of PCR MM to the samples, mix well and resuspend the beads (the beads can be difficult to resuspend, but they don't need to be completely respuspended)
4. Pipette 15 µL out of the sample to a new well containing the nuclease-free water, primer pool and i5/i7 indexes, for seperate F and R reactions
5. Run the touchdown PCR reaction using the following program on the thermal cycler:
StepTemperature TimeCycles
Initial denaturation 95 °C00:05:00 1
Touchdown PCR:
Denaturation 95 °C00:00:30 10
Annealing 68 °C-58 °C00:01:30 10 (decrease 1 °C per cycle)
Extension 72 °C00:00:30 10
PCR:
Denaturation 95 °C00:00:30 26
Annealing 58 °C00:01:30 26
Extension 72 °C00:00:30 26
Final extension 68 °C00:10:00 26
Hold 4 °C
20m
Clean up and size selection, pooling and quality control
Clean up and size selection, pooling and quality control
5m
1) After the PCR reaction is finished place the plate on the magnet for 00:05:00
2) Transfer 20 µL of the supernatant to a fresh well (transfer less than the total volume to compensate for differences in volume during pipetting).
3) Pool 10 µL of each sample in an eppendorf tubes.
4) Vortex and invert purification beads (PB) to fully resuspend.
5) Prepare at master mix of diluted PB (Note: The volumes used in the master mix is for each sample that has been pooled).
A
B
Reagent
Volume per reaction
PB
10 µL
Nuclease-free water
8,85 µL
6) Vortex and mix the diluted master mix and add 18.75 µL (per reaction) master mix to the pool and mix well
7) Seal the tubes and incubate at room temperature for 00:05:00
8) Place on magnet for 00:05:00 5 min or until clear
9) Add 3.7 µL (per reaction) of PB to a new eppendorf tube
10) Transfer 27 µL (per reaction) of the supernatant to the eppendorf tube containing PB and mix well
11) Seal the tube and incubate at room temperature for 00:05:00
12) Place the tube on a magnet for 00:05:00 or until clear
13) Remove and discard the supernatant without disrupting the beads
14) With the tube on the magnet, add fresh 80% ethanol to cover the beads without mixing and incubate 00:01:00
15) Remove the ethanol
16) Repeat steps 14 and 15 for a total of 2 washes
17) Remove any excess liquid from the tube
18) Air-dry on the magnet for 00:05:00 or until dry. The bead should not dry so long that it cracks while ethanol residues should have evaporated.
19) Remove the tube from the magnet and add 205 µL (more or less depending on desired reaction volume to elute in) resuspension buffer/water-free nuclease to the beads and mix
20) Incubate at room temperature for 00:05:00
21) Place tube on magnet for 00:02:00 or until clear
22) Transfer 200 µL of the supernatant into a fresh tube
23) Clean up two more times (start from step 12) using 0,65x ratio Ampure beads, elute in 42 µL and transfer 40 µL to a new tube before assessing size distribution again.
38m
Assess the quality of the pools using a Bioanalyzer or an equivalent instrument to see the fragment size distribution.
If there is an excess of small fragments in the library, clean up one or more times (start from step 11) using 0,65x ratio Ampure beads, elute in 42 µL and transfer 40 µL to a new tube before assessing size distribution again.