How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Sequencing by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16 How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Using the Oxford Nanopore by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16With all this ready, we opened the Nanopore flow cell, which is the 500 dollar consumable piece that goes in the sequencer.
We then had to pipette the final golden Eppendorf into the flow cell. My anxiety levels were going through the roof: Figure 4. "Oxford nanopore MinION flow cell pipette loading.".
At this point bio people start telling lab horror stories of expensive solutions being spilled and people having to recover them from fridge walls, or of how people threw away golden Eppendorfs and had to pick them out of trash bins with hundreds of others looking exactly the same etc. (but also how some discoveries were made like this). This reminded Ciro of: youtu.be/89UNPdNtOoE?t=919 Alfred Maddock's plutonium spill horror story.
Luckily this time, it worked out!
As can be seen from Video 1. "Oxford Nanopore MinION software channels pannel on Mac." the software tells us which pores are still working.
Pores go bad sooner or later randomly, until there are none left, at which point we can stop the process and throw the flow cell away.
48 hours was expected to be a reasonable time until all pores went bad, and so we called it a day, and waited for an email from the PuntSeq team telling us how things went.
We reached a yield of 16 billion base pairs out of the 30Gbp nominal maximum, which the bio people said was not bad.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Qiagen DNeasy PowerWater Kit by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16www.qiagen.com/gb/products/discovery-and-translational-research/dna-rna-purification/dna-purification/microbial-dna/dneasy-powerwater-kit (archive) Here is its documentation: www.qiagen.com/gb/resources/download.aspx?id=bb731482-874b-4241-8cf4-c15054e3a4bf&lang=en (archive).
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Qiagen QIAquick PCR Purification Kit by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16www.qiagen.com/us/products/discovery-translational-research/dna-rn-a-purification/dna-purification/dna-clean-up/qiaquick-pcr-purification-kit/#orderinginformation (archive)
Manual archive: web.archive.org/web/20190911100243/https://www.qiagen.com/us/resources/download.aspx?id=e0fab087-ea52-4c16-b79f-c224bf760c39&lang=en
Removes PCR byproducts from purified DNA.
"The Hot Troll Deviation" is the title of an episode from the popular TV show *The Big Bang Theory*, specifically season 4, episode 14. In this episode, the characters navigate various personal relationships and social dynamics. The storyline revolves around Raj's interest in a woman he meets online after he gets drunk and posts a risqué photo of himself, which leads to humorous situations. The episode explores themes of attraction and identity through its comedic lens, typical of the show's style.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Thermo Scientific Nalgene Polysulfone Reusable Bottle Top Filters by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16~8GB,
lsblk reports 7796176 * 1KB = 7983284224 bytes.They are shaped like bicornes, which is super cool, but also super impractical!
Markings: "AX ÉCOLE POLYTECHNIQUE PROMOTION X2009"
From Ubuntu 20.04 on an ext4 formatted one:With Linux Unified Key Setup + ext4 the results are similar, maybe hdparam bypasses it?
/dev/sdb:
Timing cached reads: 28656 MB in 1.99 seconds = 14421.31 MB/sec
SG_IO: bad/missing sense data, sb[]: 70 00 05 00 00 00 00 0a 00 00 00 00 20 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Timing buffered disk reads: 42 MB in 3.03 seconds = 13.88 MB/sec/dev/sdb:
Timing cached reads: 28326 MB in 1.99 seconds = 14251.55 MB/sec
SG_IO: bad/missing sense data, sb[]: 70 00 05 00 00 00 00 0a 00 00 00 00 20 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Timing buffered disk reads: 38 MB in 3.11 seconds = 12.23 MB/secgnome-disks LUKS + ext4 benchmark with default params also gives about 14 MB/s. How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Fisher Scientific UVP LM-26E Benchtop 2UV Transilluminator by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16www.bidspotter.com/en-us/auction-catalogues/bscsur/catalogue-id-bscsur10011/lot-c6605b41-1a14-40e5-a255-a5c5000866e0 (archive) Cannot exact same product on official website, but here is a similar one: www.fishersci.co.uk/shop/products/lm-26-2uv-transilluminator/12382038 (archive).
Pinned article: Introduction to the OurBigBook Project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 3. Visual Studio Code extension installation.
Figure 4. Visual Studio Code extension tree navigation.
Figure 5. Web editor. You can also edit articles on the Web editor without installing anything locally.Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. 
- Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact