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Cutting Edge: Using mobile sequencers in an academic classroom

  1. Sophie Zaaijer
  2. Columbia University Ubiquitous Genomics 2015 class
  3. Yaniv Erlich Is a corresponding author
  1. Columbia University, United States
  2. New York Genome Center, United States
  3. Center for Computational Biology and Bioinformatics, Columbia University, United States
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Cite as: eLife 2016;5:e14258 doi: 10.7554/eLife.14258
2 figures, 1 table and 7 additional files

Figures

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.

https://doi.org/10.7554/eLife.14258.002
A detailed workflow for running a hackathon using a MinION sequencer.
https://doi.org/10.7554/eLife.14258.004

Tables

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

https://doi.org/10.7554/eLife.14258.003
CompanyProductCat noPrice per unit (USD)Unit quantityAmount needed for ONT protocolCost
Covarisg-TUBE520079$275101$27.50
NEBUltra™ End Repair/dA-Tailing ModuleE7442S$225.0072 ul3 μl$9.40
AgencourtAMPure XPA63880$315.005 ml60 μl$3.78
Thermo FisherDynabeads MyOne Streptavidin C165001$475.002 mL50 μl$12
NEBBlunt/TA Ligase Master MixM0367S$95250ul50 μl$19
Tubes/ pipette-tips/H2O/
ethanol etc
~$10
ONTFlow-cell
Reagent kit
$90011$900
Projected cost per team per run:$981.68

Additional files

Supplementary file 1

Class website information.

https://doi.org/10.7554/eLife.14258.005
Supplementary file 2

Protocol for setting up a hackathon using MinION.

https://doi.org/10.7554/eLife.14258.006
Supplementary file 3

Student handout for Hackathon 1: Snack to sequence.

https://doi.org/10.7554/eLife.14258.007
Supplementary file 4

Student handout for Hackathon 2: CSI Columbia.

https://doi.org/10.7554/eLife.14258.008
Supplementary file 5

Student handout for the final project.

https://doi.org/10.7554/eLife.14258.009
Supplementary file 6

Teaching slides for Hackathon 1: Snack to sequence.

https://doi.org/10.7554/eLife.14258.010
Supplementary file 7

Teaching slides for Hackathon 2: CSI Columbia.

https://doi.org/10.7554/eLife.14258.011

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