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usegalaxy-eu/streetscience

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Anika

@erxleben

I agree with Stephan: please avoid, phenol-chloroform extraction. It smells like hell, is really dangerous and quite sure without a real lab safety instruction not allowed at all with citizens. And even if would be allowed, it needs a bit experience to handle this stuff. Don't do it.

Bérénice Batut

@bebatut

Hi. I am finally done the sequencing protocol (and templating). if anyone has some time to review it before merging would be awesome

StreetScienceCommunity/StreetScienceCommunity.github.io#60

Björn Grüning

@bgruening

Thanks Bérénice!

Wolfgang Maier

@wm75

A question you guys might have an answer to: how does nanopore sequencing compare to Illumina in terms of starting material required?

Milad Miladi

@mmiladi

Well the DNA preparation should be similar for both. The sequencing chemistry is not expensive. But big difference is that you will have the sequencer at hand, no sequencing facility required ...

Wolfgang Maier

@wm75

@milad thanks, my question was more concerning the amount of DNA though. Is that comparable to Illumina?

Milad Miladi

@mmiladi

Nanopore generally needs more DNA (in scale of µg , and not ng), as far as I understood.

Wolfgang Maier

@wm75

Yeah, that's what I expected kind of. The reason I'm asking is because a friend of mine (an eye doctor) would like to look for a possible "microbiome" inside the eye (anterior chamber behind the pupil), but I'd expect her to recover very low DNA concentrations (if anything useful at all) from this compartment.

teresa-m

@teresa-m

In the nanopore rapid sequencing kit they ask for DNA ~ 400 ng in 7.5 µl nuclease-free water

Wolfgang Maier

@wm75

This is what you're aiming for in the streetscience protocol, right. How many reads or sequenced bases do you get from that?

DonStephano

@DonStephano

Well, the big difference is the amplification step of DNA. When using a nanopore, the DNA is directly sequenced without prior amplification. For Illumina you need to do a PCR before sequencing to amplify the DNA (and introducing biases...)This means: You can start with as little as the DNA-amount from one single cell in case of Illumina. In case of the eye-microbiome I def would do Illumina-based seq...

Wolfgang Maier

@wm75

HI @DonStephano, thanks for the advice. That's pretty much what I thought, but, of course, using nanopore sequencing would add a touch of "they used fancy new technology" to the study so I thought I'll figure out if using it is a real option or not.

Bérénice Batut

@bebatut

nanopore has some kits with PCR amplification before sequencing

teresa-m

@teresa-m

Between 1000 and 2000 passed reads. But we did not let the sequencing run for a long time. But of cores, some of the reads are very long! And we our sample preparation was not always done by 'experts'.

Wolfgang Maier

@wm75

@teresa-m thanks! @bebatut Thanks for pointing that out. I guess the PCR would limit the sequenced reads length then?

I've found the description of the amplification-based kits, thank you. They have quite good information.

Milad Miladi

@mmiladi

HI @DonStephano, thanks for the advice. That's pretty much what I thought, but, of course, using nanopore sequencing would add a touch of "they used fancy new technology" to the study so I thought I'll figure out if using it is a real option or not.

Sounds really like a cool project. You may want to stick to Nanopore and make a friend whose patients cry or spit :smile: :smiling_imp:

foellmelanie

@foellmelanie

Hi all, this could be a way to find schools interested in beer sequencing: https://forschungsboerse.de/

teresa-m

@teresa-m

Cool thanks @foellmelanie !!!

Bérénice Batut

@bebatut

New paper probably interesting for us: "An educational guide for nanopore sequencing in the classroom”

teresa-m

@teresa-m

Hey, if someone wants to join us today, we meet at 17:10 at mm! for some food and at 18:00 at the coworking. :-)

teresa-m

@teresa-m

Hey, here is the short presentation to introduce us at the galaxy workshop! Feel free to change or propose changes: https://docs.google.com/presentation/d/1nNypWyQI5ZabwNX0v4kPl_t3TcysEFb2BFmBK0HVBH0/edit#slide=id.g5c67b9aa23_0_100

Paramartina

@Paramartina

I like the presentation!

Milad Miladi

@mmiladi

Looks very good Teresa. If you want to add something hot, this outlet news can be relevant:

https://www.telegraph.co.uk/technology/2020/01/31/pocket-sized-dna-kits-oxford-could-help-track-coronavirus/

teresa-m

@teresa-m

thanks I will inclued this news! :-)

Anika

@erxleben

@teresa-m we are in the compute center, room -100 from tomorrow on. Due to safety problem we had to leave Werthmanstrasse

teresa-m

@teresa-m

Ok super, thanks a lot!

DonStephano

@DonStephano

https://www.pr.uni-freiburg.de/pm-en/online-magazine/teaching-and-learning/sharing-knowledge-between-campus-and-citizens?set_language=en

maybe we could apply? 5000 EUR maximun...

teresa-m

@teresa-m

Cool thanks a lot. I guess at the moment we would not need new funding. But it would be maybe a good way to get some notice of our project inside the university! :-)

Milad Miladi

@mmiladi

side fact: Today I got prescribed a pill that turned out to be Saccharomyces cerevisiae capsules! I didn't know that it can used in medicine and also rarely can become a pathogen . :-) From wikipedia:

Saccharomyces cerevisiae is used as a probiotic in humans and animals. Especially, a strain Saccharomyces cerevisiae var. boulardii is industrially manufactured and clinically used as a medication.[...]

Björn Grüning

@bgruening

you could also drink just more beer as we know ;)

Milad Miladi

@mmiladi

https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae#Direct_use_in_medicine

you could also drink just more beer as we know ;)

Exactly, then I thought about the story about boiling beer as a remedy :)

Bérénice Batut

@bebatut

Interesting game: https://phys.org/news/2020-02-lab-scientific-life.amp?__twitter_impression=true

F. H.

@heylf

https://www.nature.com/collections/eccfeecfae

Florian Eggenhofer

@eggzilla

Hey, when will the Meeting start tomorrow? Anika and me will join, however we cannot start before 7pm

teresa-m

@teresa-m

ok, In the morning I wrote that we will start at 18:30. But we can also start later! I will send another e-mail. Sorry for the many e-mails! I will try to improve on that. :-)

teresa-m

@teresa-m

https://docs.google.com/document/d/1WZuWBEQalKMh2YeZ4aaQdqFAbBO-u6_P6V7MH24FwJE/edit

teresa-m

@teresa-m

Extraction-Protocol-Thermo-Scientific-Yeast-DNA-extraction-kit-version2.docx

Milad Miladi

@mmiladi

https://nanoporetech.com/events/nanopore-sequencing-sars-cov-2-genome-webinars?utm_campaign=Coronavirus%202020&utm_content=124818708&utm_medium=social&utm_source=linkedin&hss_channel=lcp-340169

teresa-m

@teresa-m

We will meet tomorrow at 18:00:

https://uni-freiburg.zoom.us/j/95013035116

Meeting-ID: 950 1303 5116
Passwort: 7RQ0!FGXy

looking forward to meet you :-)

teresa-m

@teresa-m

Dear All, since it is my birthday next Tuesday. I would be happy if we shift the meeting one week. Sorry I did not check the calender last time when we set the meeting. Hope everone is ok with this.

teresa-m

@teresa-m

*everyone