Illumina DNA Prep, (M) Tagmentation, 24 sample kit (Illumina 20060060, originally 20018704) or 96 sample kit (20060059, originally 20018705). Note: these products were previously known as Nextera DNA Flex Library Prep.
Custom dual index primers (see supplemental). Alternatively, IDT for Illumina DNA/RNA Unique Dual Indexes Tagmentation (96 Indexes, 96 Samples), Set A (Illumina 20027213), Set B (20027214), Set C (20027215), or Set D (20027216).
Custom tagmentation buffer (see 'before start', 2x TMP: 20 mM Tris-HCl pH 8, 10 mM MgCl2, 16% PEG 8,000).
Tris-HCl pH 8 (e.g. UltraPure 1M Tris-HCI, pH 8.0, Thermo Fisher Scientific 15568025).
Magnesium chloride (e.g. 1 M MgCl2, Thermo Fisher Scientific AM9530G).
Poly(ethylene glycol) 8,000 (e.g. PEG 8,000 BioUltra, Merck 89510-1KG-F).
Nuclease-free water (e.g. UltraPure DNase/RNase-Free Distilled Water, Thermo Fisher Scientific 10977015).
dsDNA Quantification High Sensitivity Kit (for microplate reader) (BioDynami 40540H). The broad range assay kit may be required depending on the concentration of samples (BioDynami 40540B). Alternatives: Quant-iT dsDNA Assay Kit, high sensitivity (HS) and broad range (BR) (Thermo Fisher Scientific Q33120 and Q33130 respectively).
dsDNA Quantification High Sensitivity Kit (BioDynami 40042L) (required if doing protocol in low-throughput). The broad range assay kit may be required depending on the concentration of samples (BioDynami 40041L). Alternatives: Qubit dsDNA Quantification Assay Kits, high sensitivity (HS) and broad range (BR) (Thermo Fisher Scientific Q32854 and Q32853 respectively).
Qubit assay tubes (Thermo Fisher Scientific Q32856).
Q5 High-Fidelity DNA Polymerase (New England BioLabs M0491L).
10 mM dNTPs (New England BioLabs N0447).
70% ethanol (analytical grade or higher).
AMPure XP Reagent, SPRI paramagnetic beads (Beckman Coulter A63881) (or equivalent beads). May not be needed, depends on clean-up strategy.
96-well half skirt PCR microplate (e.g. Axygen Scientific PCR-96M2-HS-C).
96-well microplate suitable for fluorescent readings, e.g. Microplate, 96 well, PS, half area, black, med. binding (Greiner Bio-One 675076), or alternatively, 96-well PCR microplate white, Roche 480 light cycler (Axygen Scientific PCR-96-LC480-W-NF).
384-well microplate (e.g. 4titude FrameStar 4ti-0384/B).
PCR-grade adhesive seals for microplates (e.g. Thermo Fisher Scientific AB0558).
2 mL SC micro tube PCR-PT (Starstedt 72694.406) (or equivalent, for PerkinElmer automated workstations)
1.5 mL microcentrifuge tubes (e.g. Eppendorf tubes).
15 mL and/or 50 mL centrifuge tubes (e.g. Falcon tubes).
FLUOstar Omega fluorescent microplate reader (BMG Labtech), or equivalent, e.g. Infinite M1000 PRO (Tecan).
PCR machine for 96-well microplate.
PCR machine for 384-well microplate, or a microplate heat block.
Magnetic rack for 1.5 mL microcentrifuge tubes.
Qubit Fluorometer (Thermo Fisher Scientific).
(Optional) JANUS automated workstation, such as NGS express or JANUS G3, including relevant accessories; reagent reservoirs, plate adaptor support tiles, 25 and 175 µL filtered tips (PerkinElmer).
(Optional) PippinHT (Sage Science), including 2% agarose casette and reagents.
(Optional) High sensitive electrophoresis system, such as LabChip GX devices (PerkinElmer) or Bioanalyzer/TapeStation devices (Agilent Technologies).