Using Basic MinION Starter Pack in remote area for soil samples

SuzuBell · 02-13-2019, 05:43 PM

I am not experienced with metagenomics/metatranscriptomics/soil microbiology/Nanopore technology, so please forgive if this post is misguided

I plan to conduct field work in a (slightly) remote area. I will live there (at a basic research facility) for 2 weeks. I hope to conduct a simple proof-of-concept study there that involves me:

1) collecting soil samples,
2) using the Basic MinION Starter Pack to study the soil composition directly at the research facility,
3) checking the data for methane-producing organisms or activities.

I have two questions related to this goal.

1) To perform step (2) above, what is a *complete list* of resources I would need at minimum? The Basic MinION Starter Pack (https://store.nanoporetech.com/configure-minion-basic) comes with 1 MinION, 2 flow cells, and 1 sequencing kit. Is this actually all that is needed besides the soil sample? Or, are there other (especially costly) items needed? For instance, will I need a refrigerator (and at what temperature)? Will I need a centrifuge? Will I need other specialized tools? I am aiming to keep the costs not much more than the $1,000 needed for the Starter Pack and am unsure if that is unrealistic. The research facility has extremely basic tools and I would need to ask in advance for anything!

2) Scientists have found that the soil in this area produced methane after the introduction of growth medium, suggesting that methane was being given off by an organism. I am hoping to investigate that further (in some way) using the MinIon Starter Pack. So, I am interested in looking for, for example, methane-producing genes, metabolites, or organisms. Is it even possible that the Basic MinION Starter Pack could be used to look for such data?

This is really supposed to be a modest learning project that have some basic results in a few weeks at a cost not much more than $1,000. Feasible or fantasy?

Thank you for sharing your advice!

Marc_Jones · 02-18-2019, 03:44 AM

Which library prep method are you using? Have you read the protocol?

gringer · 04-07-2019, 03:43 PM

The Starter Pack is not sufficient for doing multiple samples. In ONT's infinite wisdom, they decided to put the rapid kit as an option, rather than the rapid barcoding kit (despite them having essentially identical sample preparation protocols).

If you want to do more than a single sample as cheap as possible, you'll need to get either a wash kit (to run multiple samples on the same flow cell, with some carryover), or a rapid barcoding kit (to run multiple samples within the same sequencing run).

The rapid barcoding kit doesn't need any other reagents except for distilled water. A fridge/freezer is a good idea (fridge ideally at 8 degrees Celsius for the flow cells; anything below 4 will kill the flow cells).

There are a few things that are nice to have. Have a look at the "3rd party materials" section for the rapid kits in the store:

https://store.nanoporetech.com/catal...t/category/28/

If you want to see the things that I consider to be a bare minimum, see my linux.conf.au talk:

https://www.youtube.com/watch?v=CHCAb-PAqUI

The hardest part is extracting the DNA in the first place. I recommend sorting that out first before getting any flow cells.

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02-13-2019, 05:43 PM	#1
SuzuBell Member Location: U.S.A Join Date: Nov 2013 Posts: 23	Using Basic MinION Starter Pack in remote area for soil samples I am not experienced with metagenomics/metatranscriptomics/soil microbiology/Nanopore technology, so please forgive if this post is misguided I plan to conduct field work in a (slightly) remote area. I will live there (at a basic research facility) for 2 weeks. I hope to conduct a simple proof-of-concept study there that involves me: 1) collecting soil samples, 2) using the Basic MinION Starter Pack to study the soil composition directly at the research facility, 3) checking the data for methane-producing organisms or activities. I have two questions related to this goal. 1) To perform step (2) above, what is a complete list of resources I would need at minimum? The Basic MinION Starter Pack (https://store.nanoporetech.com/configure-minion-basic) comes with 1 MinION, 2 flow cells, and 1 sequencing kit. Is this actually all that is needed besides the soil sample? Or, are there other (especially costly) items needed? For instance, will I need a refrigerator (and at what temperature)? Will I need a centrifuge? Will I need other specialized tools? I am aiming to keep the costs not much more than the $1,000 needed for the Starter Pack and am unsure if that is unrealistic. The research facility has extremely basic tools and I would need to ask in advance for anything! 2) Scientists have found that the soil in this area produced methane after the introduction of growth medium, suggesting that methane was being given off by an organism. I am hoping to investigate that further (in some way) using the MinIon Starter Pack. So, I am interested in looking for, for example, methane-producing genes, metabolites, or organisms. Is it even possible that the Basic MinION Starter Pack could be used to look for such data? This is really supposed to be a modest learning project that have some basic results in a few weeks at a cost not much more than $1,000. Feasible or fantasy? Thank you for sharing your advice!

02-18-2019, 03:44 AM	#2
Marc_Jones Member Location: UK Join Date: Jun 2017 Posts: 10	Which library prep method are you using? Have you read the protocol?

04-07-2019, 03:43 PM	#3
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 838	The Starter Pack is not sufficient for doing multiple samples. In ONT's infinite wisdom, they decided to put the rapid kit as an option, rather than the rapid barcoding kit (despite them having essentially identical sample preparation protocols). If you want to do more than a single sample as cheap as possible, you'll need to get either a wash kit (to run multiple samples on the same flow cell, with some carryover), or a rapid barcoding kit (to run multiple samples within the same sequencing run). The rapid barcoding kit doesn't need any other reagents except for distilled water. A fridge/freezer is a good idea (fridge ideally at 8 degrees Celsius for the flow cells; anything below 4 will kill the flow cells). There are a few things that are nice to have. Have a look at the "3rd party materials" section for the rapid kits in the store: https://store.nanoporetech.com/catal...t/category/28/ If you want to see the things that I consider to be a bare minimum, see my linux.conf.au talk: https://www.youtube.com/watch?v=CHCAb-PAqUI The hardest part is extracting the DNA in the first place. I recommend sorting that out first before getting any flow cells.