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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
...
DNA
DNA sequencing
DNA sequencing company
Oxford Nanopore Technologies
Oxford Nanopore Technologies product
Oxford Nanopore MinION
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The best articles by Ciro Santilli
,
DNA sequencing
,
Metagenomics
,
Polymerase chain reaction
Words: 3k
Articles: 30
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
30
1.
Experiment background
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
243
2.
Overview of the experiment
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
590
1
2.1.
Why Oxford Nanopore was used instead of Illumina for the sequencing
Overview of the experiment
190
3.
Sample collection
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
140
4.
DNA extraction
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
532
2
4.1.
Filtration with vacuum pump
DNA extraction
175
4.2.
Post filtration purification
DNA extraction
252
5.
PCR
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
604
1
5.1.
PCR verification with gel electrophoresis
PCR
263
6.
Sequencing
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
402
2
6.1.
Pre-sequencing preparation
Sequencing
143
6.2.
Using the Oxford Nanopore
Sequencing
245
7.
Bioinformatics
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
239
8.
Conclusions
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
134
9.
Protocols used
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
94
3
9.1.
Qiagen DNeasy PowerWater Kit
Protocols used
19
9.2.
Qiagen QIAquick PCR Purification Kit
Protocols used
11
9.3.
Oxford Nanopore SQK-LSK109 Ligation Sequencing Kit
Protocols used
28
10.
Equipment used
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
77
10
10.1.
Thermo Scientific Nalgene Polysulfone Reusable Bottle Top Filters
Equipment used
29
10.2.
KNF Laboport series laboratory vacuum pump
Equipment used
3
10.3.
Scientific Industries Inc. Vortex-Genie 2
Equipment used
3
10.4.
VWR Micro Star 17 microcentrifuge
Equipment used
3
10.5.
VELP Scientifica WIZARD IR Infrared Vortex Mixer
Equipment used
3
10.6.
Marshal Scientific MJ Research PTC-200 Thermal Cycler
Equipment used
3
10.7.
GE MagRack 6
Equipment used
3
10.8.
BTLab Systems Mini Centrifuge
Equipment used
4
10.9.
Fisher Scientific UVP LM-26E Benchtop 2UV Transilluminator
Equipment used
19
10.10.
Biochrom SimpliNano spectrophotometer
Equipment used
7
11.
External links to this page
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
21
Ancestors
(12)
Oxford Nanopore MinION
Oxford Nanopore Technologies product
Oxford Nanopore Technologies
DNA sequencing company
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Molecular biology
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The best articles by Ciro Santilli
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Exams and homework are useless, only projects matter
Metagenomics
Oxford Nanopore MinION
Polymerase chain reaction
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