Cutting Edge: Using mobile sequencers in an academic classroom
- Columbia University, United States
- New York Genome Center, United States
- Center for Computational Biology and Bioinformatics, Columbia University, United States
Figures
Figure 1
The Ubiquitous Genomics class.
(A) Illumina MiSeq benchtop sequencer (left) and the MinION sequencer made by Oxford Nanopore Technologies (right; red rectangle). (B) The class during a hackathon.
Figure 2
A detailed workflow for running a hackathon using a MinION sequencer.
https://doi.org/10.7554/eLife.14258.004Tables
Table 1
MinION consumables:Total cost estimate (in US Dollars) is for one MinION run per team. For the complete list of equipment and consumables required for organizing a hackathon, please see the following link: https://nanoporetech.com/uploads/community/Equipment_and_consumables_vC_with_FAQ_Sep2015.pdf
| Company | Product | Cat no | Price per unit (USD) | Unit quantity | Amount needed for ONT protocol | Cost |
|---|---|---|---|---|---|---|
| Covaris | g-TUBE | 520079 | $275 | 10 | 1 | $27.50 |
| NEB | Ultra™ End Repair/dA-Tailing Module | E7442S | $225.00 | 72 ul | 3 μl | $9.40 |
| Agencourt | AMPure XP | A63880 | $315.00 | 5 ml | 60 μl | $3.78 |
| Thermo Fisher | Dynabeads MyOne Streptavidin C1 | 65001 | $475.00 | 2 mL | 50 μl | $12 |
| NEB | Blunt/TA Ligase Master Mix | M0367S | $95 | 250ul | 50 μl | $19 |
| Tubes/ pipette-tips/H2O/ ethanol etc | ~$10 | |||||
| ONT | Flow-cell Reagent kit | $900 | 1 | 1 | $900 | |
| Projected cost per team per run: | $981.68 | |||||
Additional files
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Supplementary file 1
Class website information.
- https://doi.org/10.7554/eLife.14258.005
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Supplementary file 2
Protocol for setting up a hackathon using MinION.
- https://doi.org/10.7554/eLife.14258.006
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Supplementary file 3
Student handout for Hackathon 1: Snack to sequence.
- https://doi.org/10.7554/eLife.14258.007
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Supplementary file 4
Student handout for Hackathon 2: CSI Columbia.
- https://doi.org/10.7554/eLife.14258.008
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Supplementary file 5
Student handout for the final project.
- https://doi.org/10.7554/eLife.14258.009
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Supplementary file 6
Teaching slides for Hackathon 1: Snack to sequence.
- https://doi.org/10.7554/eLife.14258.010
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Supplementary file 7
Teaching slides for Hackathon 2: CSI Columbia.
- https://doi.org/10.7554/eLife.14258.011
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Cutting Edge: Using mobile sequencers in an academic classroom
eLife 5:e14258.
https://doi.org/10.7554/eLife.14258
