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WET LAB DNA Barcoding: From Samples to Sequences - Northwest ...

WET LAB DNA Barcoding: From Samples to Sequences - Northwest ...

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<strong>WET</strong> <strong>LAB</strong><br />

Lab 1: <strong>DNA</strong> Purification for <strong>DNA</strong> <strong>Barcoding</strong><br />

<strong>DNA</strong> purification reagents or kit<br />

Recommended: ZR Genomic <strong>DNA</strong>-Tissue MiniPrep. Available from Zymo Research.<br />

Item #D3050 (50 reactions) or D3051 (200 reactions) http://www.zymoresearch.com/<br />

<strong>Samples</strong> (such as fish, meat, insects, etc.)<br />

[Note: See Obtaining <strong>Samples</strong> for <strong>DNA</strong> <strong>Barcoding</strong> below for more information.]<br />

Nuclease-free, ultra-pure (i.e., nano-pure) or distilled water<br />

Recommended: Nuclease-Free Water. Available from QIAGEN. Item #129115 (1000 ml)<br />

www.qiagen.com/<br />

Class set of Student Handout—<strong>DNA</strong> Purification for <strong>DNA</strong> <strong>Barcoding</strong><br />

Razor blades (or alternative means <strong>to</strong> shred tissue, such as plastic butter knives) and<br />

plastic dishes or small plates<br />

Vortexers [Note: Not necessary, but highly recommended.]<br />

Quantity<br />

1 reaction per student<br />

1 per student<br />

Approximately 100 μl<br />

per student<br />

1 per student (class set)<br />

1 per student<br />

1–2 per class (up <strong>to</strong> 1 per group)<br />

55°C Water bath or incuba<strong>to</strong>r 1<br />

1.7 ml microfuge tubes 2 per student<br />

Lab 2: Copying the <strong>DNA</strong> <strong>Barcoding</strong> Gene<br />

Using Polymerase Chain Reaction (PCR)<br />

PCR reagents or kit<br />

Recommended: GE Healthcare* illustra* PuRe Taq Ready-To-Go* PCR Beads 0.2 ml<br />

tube w/hinged cap. Available from Fisher Scientific. Item #46-001-014<br />

http://www.fishersci.com/<br />

Nuclease-free, ultra-pure (i.e., nano-pure) or distilled water<br />

Recommended: Nuclease-Free Water. Available from QIAGEN. Item #129115 (1000 ml)<br />

www.qiagen.com/<br />

PCR barcoding primer poolss<br />

Available from NWABR –OR– Primers may be ordered from a commercial producer,<br />

such as Eurofins MWG Operon. http://www.operon.com<br />

Primer sequences are available in Ivanova et al., 2007 (see Resources).<br />

Class set of Student Handout–Copying the <strong>DNA</strong> <strong>Barcoding</strong> Gene Using Polymerase<br />

Chain Reaction (PCR)<br />

Quantity<br />

1 per student<br />

Approximately 50 μl per student<br />

5.0 μl per student<br />

1 per student (class set)<br />

Thermocycler for PCR 1<br />

Racks <strong>to</strong> hold 0.2 ml PCR tubes (such as empty P200 or P1000 tip box bases)<br />

Ice buckets with ice<br />

1 per student –OR– 1 per group<br />

1 per group<br />

1.7 ml microfuge tubes 1 per student<br />

Wet Lab – <strong>DNA</strong> <strong>Barcoding</strong>: <strong>From</strong> <strong>Samples</strong> <strong>to</strong> <strong>Sequences</strong><br />

321<br />

©<strong>Northwest</strong> Association for Biomedical Research—Updated Oc<strong>to</strong>ber 2012

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