User-Supplied Consumables & Equipment
Make sure that you have the required consumables and equipment before starting the protocol.
Some items are required only for specific workflows. These items are specified in separate tables.
The protocol has been optimized and validated using the items listed. Comparable performance is not guaranteed when using alternate consumables and equipment.
Consumables
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Consumable |
Supplier |
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1.7 ml microcentrifuge tubes |
General lab supplier |
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10 µl pipette tips |
General lab supplier |
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20 µl pipette tips |
General lab supplier |
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200 µl pipette tips |
General lab supplier |
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1000 µl pipette tips |
General lab supplier |
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96-well 0.8 ml polypropylene deepwell storage plate (MIDI plate) |
Thermo Fisher Scientific, part # AB-0859 |
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Nuclease-free water |
General lab supplier |
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Conical centrifuge tubes (15 ml or 50 ml) |
General lab supplier |
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Eppendorf twin.tec 96-well LoBind PCR plate, skirted |
Eppendorf, catalog # 0030129512 |
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Hard-Shell 96-well PCR plates |
Bio-Rad, catalog # HSP-9601 |
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Microseal 'B' adhesive seals |
Bio-Rad, catalog # MSB-1001 |
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Microseal 'F' foil seals |
Bio-Rad, catalog # MSF-1001 |
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RNase/DNase-free 8-tube strips and caps |
General lab supplier |
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RNase/DNase-free multichannel reagent reservoirs, disposable |
VWR, catalog # 89094-658 |
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Ethanol 200 proof (absolute) for molecular biology (500 ml) |
Sigma-Aldrich, product # E7023 |
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Illumina Purification Beads |
Illumina, 1 x 100 ml, catalog # 20060057 Illumina, 4 x 100 ml, catalog # 20060058 |
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Qubit Assay Tubes |
Thermo Fisher Scientific, catalog # Q32856 |
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One of the following kits for quantification:
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One of the following suppliers:
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One of the following kits, depending on quantification method:
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One of the following suppliers, depending on instrument:
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Tris-HCl 10 mM, pH 8.5 |
General lab supplier |
DNA Extraction Consumables
Make sure that you have the required consumables before starting the DNA extraction protocol.
|
Consumable |
Supplier |
|---|---|
|
Collection tubes, 2.0 ml |
Zymo Research, catalog # C1001 |
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Microcentrifuge tubes, 1.5 ml |
General lab supplier |
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Microcentrifuge tubes, 2.0 ml |
General lab supplier |
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ZR BashingBead Lysis Tubes |
Zymo Research, catalog # S6012-50 |
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Zymo-Spin III-Filters |
Zymo Research, catalog # C1057-50 |
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Zymo-Spin IC-S Columns |
Zymo Research, catalog # C1015 |
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BashingBead Buffer |
Zymo Research, catalog # D6001-3 |
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Clearing Beads |
Zymo Research, catalog # D3061-2-1 |
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Genomic Lysis Buffer |
Zymo Research, catalog # D3004-1 |
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Urine Conditioning Buffer (UCB) |
Zymo Research, catalog # D3061-1 |
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Urine DNA Prep Buffer |
Zymo Research, catalog # D3061-4-10 |
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Urine DNA Wash Buffer (Concentrate) |
Zymo Research, catalog # D3061-5-12 |
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1X DNA/RNA Shield reagent |
Zymo Research, catalog # R1100-50, or R1100-250 |
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ZymoBIOMICS Microbial Community Standard |
Zymo Research, catalog # D6300 |
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Urine Conditioning Buffer (UCB) |
Zymo Research, catalog # D3061-1 |
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Molecular Biology Grade (MBG) Water |
General lab supplier |
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T7 Phage |
Microbiologics, catalog # T7-UP-LEX |
Equipment
|
Equipment |
Supplier |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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10 µl multichannel pipette |
General lab supplier |
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10 µl single channel pipette |
General lab supplier |
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20 µl multichannel pipette |
General lab supplier |
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20 µl single channel pipette |
General lab supplier |
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200 µl multichannel pipette |
General lab supplier |
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200 µl single channel pipette |
General lab supplier |
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1000 µl single channel pipette |
General lab supplier |
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Bio-Rad C1000 Touch Thermal Cycler with 96–Deep Well Reaction Module |
Bio-Rad, part #
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Magnetic Stand-96 |
Thermo Fisher Scientific, catalog # AM 10027 |
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Microplate centrifuge |
General lab supplier |
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Microcentrifuge |
General lab supplier |
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Heat block (able to accommodate 2 ml microtubes and 60°C) |
General lab supplier |
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Adhesive seal roller |
General lab supplier |
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Biosafety Cabinet PCR workstation |
General lab supplier |
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Qubit Fluorometer 3.0 |
Thermo Fisher Scientific, catalog # Q33216, or Q33217 |
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Vortexer |
General lab supplier |
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One of the following analyzers: Advanced Analytical:
Agilent Technologies:
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Advanced Analytical:
Agilent Technologies:
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*No longer available for purchase.
DNA Extraction Equipment
Make sure that you have the required equipment before starting the DNA extraction protocol.
|
Equipment |
Supplier |
|---|---|
|
FastPrep-24 5G bead beating grinder and lysis system |
MP Bio, catalog # 6005500 |
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1000 µl multi-channel pipettes |
General lab supplier |
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QuickPrep adapter for 24 x 2 ml tube holder for FastPrep-24 |
MP Bio, catalog # 6005512 |
Equipment for Plate Workflow
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Equipment |
Supplier |
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|---|---|---|---|---|---|---|---|
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Magnetic Stand-96 |
Thermo Fisher Scientific, catalog # AM10027 |
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High-Speed Microplate Shaker |
BioShake iQ High-Speed Thermal Mixer
BioShake XP High-Speed Thermal Mixer
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Microplate centrifuge |
General lab supplier |
The following table lists the recommended settings for the thermal cycler. If your lab has a thermal cycler that is not listed, validate the thermal cycler before performing the protocol.
|
Thermal Cycler |
Temp Mode |
Lid Temp |
Vessel Type |
|---|---|---|---|
|
Bio-Rad C1000 Touch Thermal Cycler with 96–Deep Well Reaction Module (part # 1851197) |
Calculated |
Heated |
Plate |
