Introduction
This protocol is a low-cost alternative to the Illumina DNA Prep protocol (previously Nextera DNA Flex). The paper describing Hackflex can be found here. Hack Flex is similar to the official protocol, but uses diluted Bead-Linked Transposomes and lab-made buffers.
The Illumina DNA Prep protocol can be found here.
Reagents
Reagent | Vendor | Catalog | Storage |
Illumina DNA Prep Kit | Illumina | 20060059 | Various |
IDT for Illumina DNA/RNA UD Indexes Set A | Illumina | 20027213 | -20°C |
IDT for Illumina DNA/RNA UD Indexes Set B | Illumina | 20027214 | -20°C |
IDT for Illumina DNA/RNA UD Indexes Set C | Illumina | 20042666 | -20°C |
IDT for Illumina DNA/RNA UD Indexes Set D | Illumina | 20042667 | -20°C |
80% Ethanol, freshly prepared | NA | NA | RT |
Molecular-Grade (Nuclease-Free) Water | Sigma | W4502-1L | RT |
Tris HCI Buffer, pH 7.6, 1 M | Crystalgen | 221-230 | 4°C |
MgCl2, 1 M | VWR | E525-100ML | RT |
N,N-DIMETHYLFORMAMIDE >99%, liquid | Sigma | D4551-250ML | RT, in flammable cabinet |
UltraPure 10% SDS | ThermoFisher | 15553027 | RT |
PrimeSTAR GXL DNA Polymerase Kit | Takara | R050A | -20°C |
Tris-EDTA (TE) Buffer | FisherScientific | BP2473-1 | RT |
SPRI (Homemade) or AmpureXP Beads | 4°C |
Protocol
Prepare Reagents
Bring to room temperature. Vortex to mix. Do not centrifuge before pipetting.
(Split between 2 50 mL conicals)
Bring to room temperature. Vortex to mix.
Reagent | [Stock] | [Final] | Volume (ml) |
Tris HCI Buffer, pH 7.6, 1 M | 1 M | 20 mM | 1 |
MgCl, 1 M | 1 M | 20 mM | 1 |
N,N-DIMETHYLFORMAMIDE >99%, liquid | >99% | 50% | 25 |
Molecular Grade Water | NA | NA | 23 |
Total | NA | NA | 50 |
If precipitates are observed, heat at 37°C for 10 minutes and then vortex until dissolved.
Reagent | [Stock] | [Final] | Volume (ml) |
Ultrapure SDS | 10% | 0.2% | 1 |
Molecular Grade Water | NA | NA | 49 |
Total | NA | NA | 50 |
Filter through 0.22 um filter before use. Use at room temperature
Reagent | [Stock] | [Final] | Amount |
PEG 8000 | Solid | 10% | 25 g |
NaCl | 5 M | 0.25 M | 12.5 ml |
Tris-EDTA (TE) buffer (10 mM Tris and 1 mM EDTA) | 1X | NA | to 250 ml |
Total | NA | NA | 250 ml |
Thaw at room temperature. Spin briefly before use.
Thaw and bring to room temperature. Vortex to mix.
Equilibrate to RT for at least 30 min. Vortex and invert to mix.
Tagment DNA
Reagent | Volume | 96 Samples | x Samples |
1:50 BLT | 11 ul | 1,056 ul | |
LTB | 27.5 ul | 2,640 ul |
Post-Tagmentation Cleanup
Amplify Tagmented DNA
Reagent | Volume (ul) | 96 Samples | X Samples |
5x GXL Buffer | 11 | 1,056 | |
25 mM dNTPs | 4.4 | 422.2 | |
PrimeStar GXL Polymerase | 2.2 | 211.2 | |
Nuclease-free Water | 20.9 | 2,006.4 |
- 68°C for 3 min
- 98°C for 3 min
- 12 cycles of:
- 98°C for 45 sec
- 62°C for 30 sec
- 68°C for 2 min
- 68°C for 1 min
- 10°C hold
Clean Up Libraries
Due to Hackflex’s lower PCR reaction volume, you may get slightly less supernatant here and in the proceeding steps.
Quality Check
- Libraries with DNA Inputs of 100-500 ng generated in the same experiments do not require quantification individually. These can be pooled in a microcentrifuge tube. Add 5 ul of each library (up to 384), vortex to mix, and centrifuge briefly before quantifying the pool.
- Libraries with DNA Inputs of <100 ng require individual quantification.
- Use the HS DNA 5000 or HS DNA 1000 tape and the appropriate reagent buffer. A successful library preparation will have a peak around 500bp. See below for example traces.
- Quantify the sample with the HS DNA Qubit kit.
Standard Nextera Flex Tapestation Trace
HackFlex Tapestation Trace