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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
Oxford Nanopore MinION
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Metagenomics
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This article gives an idea of how this kind of biological experiment feels like to a
software engineer
who has never done any
biology
like
Ciro Santilli
.
Table of contents
3k
1. Experiment background
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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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2. Overview of the experiment
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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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2.1. Why Oxford Nanopore was used instead of Illumina for the sequencing
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Overview of the experiment
190
3. Sample collection
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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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4. DNA extraction
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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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4.1. Filtration with vacuum pump
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DNA extraction
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4.2. Post filtration purification
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DNA extraction
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5. PCR
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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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5.1. PCR verification with gel electrophoresis
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PCR
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6. Sequencing
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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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6.1. Pre-sequencing preparation
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Sequencing
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6.2. Using the Oxford Nanopore
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Sequencing
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7. Bioinformatics
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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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8. Conclusions
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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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9. Protocols used
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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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9.1. Qiagen DNeasy PowerWater Kit
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Protocols used
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9.2. Qiagen QIAquick PCR Purification Kit
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Protocols used
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9.3. Oxford Nanopore SQK-LSK109 Ligation Sequencing Kit
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Protocols used
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10. Equipment used
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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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10.1. Thermo Scientific Nalgene Polysulfone Reusable Bottle Top Filters
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Equipment used
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10.2. KNF Laboport series laboratory vacuum pump
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Equipment used
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10.3. Scientific Industries Inc. Vortex-Genie 2
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Equipment used
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10.4. VWR Micro Star 17 microcentrifuge
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Equipment used
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10.5. VELP Scientifica WIZARD IR Infrared Vortex Mixer
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Equipment used
3
10.6. Marshal Scientific MJ Research PTC-200 Thermal Cycler
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Equipment used
3
10.7. GE MagRack 6
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Equipment used
3
10.8. BTLab Systems Mini Centrifuge
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Equipment used
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10.9. Fisher Scientific UVP LM-26E Benchtop 2UV Transilluminator
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Equipment used
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10.10. Biochrom SimpliNano spectrophotometer
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Equipment used
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11. External links to this page
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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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