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    Paramartina
    @Paramartina
    we had S. cerevisia as positive control - and got nice results. for the yeast from la trappe not so much
    Milad Miladi
    @mmiladi
    Thanks much Martina. How would this compare with the older method? Would you recommend to use the new kit?
    DonStephano
    @DonStephano
    Thanks for testing the kit! Good to know that it works as it should. Does anyone know how much DNA we used for the library prep?! I mean if there is enough (I know, the more the better) to go on with the library prep, I definitely would prefer the kit based extraction... And a concentration of at least 50 ng/µl doesn't sound bad
    teresa-m
    @teresa-m
    Hey, I am not good at these concentration calculations. But for the last sequencing, we used the Rothaus (40 ng/µl). And the sequencing protocol askes for: DNA ~ 400 ng should be in 7.5 µl nuclease-free water. Does this answer your question? Did you get the 50 ng/µl from Martinas numbers?
    Paramartina
    @Paramartina
    sorry, my post is a bit mixed up. yes, we had as lowest value 50 ng/µl. The quality is not great according to the Nanodrop and i can't detect the La Trappe DNA on the agarose gel, but that is consistent with the comparatively low amount (when you look at Saccharomyces with >800ng/µl) which by the way looks beautiful.
    So i would like to try again improving a bit some incubation steps but the ulitmate test will be to use DNA extracted with the kit for sequencing to really see how well it works. For sure the possibilities for errors is reduced with the kit ;)
    teresa-m
    @teresa-m
    So tomorrow we can also discuss if we do some sequencing soon. :-)
    Bérénice Batut
    @bebatut
    Hi. Illumina Foundation and Discovery Education created nice educational resources that could be useful for us: https://www.dnadecoded.org/educator-resources.html
    Bérénice Batut
    @bebatut
    sounds interesting. thanks! I register :smile:
    teresa-m
    @teresa-m
    cool me too! It is at 21:00 for us?
    Bérénice Batut
    @bebatut
    yes
    it will be recorded. so we can still watch it later
    teresa-m
    @teresa-m
    ok cool. :-)
    Bérénice Batut
    @bebatut
    Hi @/all. quick reminder. please fill the doodle (https://doodle.com/poll/smw5v2irarw2mbiq) to find a date for our next sequencing day together. thanks :smile:
    DonStephano
    @DonStephano
    So, next sunday?!
    Bérénice Batut
    @bebatut
    I am waiting for the answer of @Paramartina
    to know if we can also get a room
    Bérénice Batut
    @bebatut
    also
    Bérénice Batut
    @bebatut
    Hi. it is too tight to organize sth for this weekend (sorry @DonStephano). we try to organize the day for next weekend
    Bérénice Batut
    @bebatut
    Hi, here are the flyers (in english and german) that we would like to send around
    german_a5.pdf
    english_a5.pdf
    we would love to have some feedback on them :smile:
    teresa-m
    @teresa-m
    Cool thanks a lot!
    Milad Miladi
    @mmiladi
    Thanks much B!
    Anika
    @erxleben
    Hi all, could I borrow the minion for just showing the device? I would need to pick it up on Monday (where?)
    teresa-m
    @teresa-m
    Ja of corse. It is in Martinas Lab but we can take it with us tomorow.
    Anika
    @erxleben
    Would be cool for the NGS lecture on Tuesday
    Thank you 😊
    teresa-m
    @teresa-m
    It is back in my office!
    teresa-m
    @teresa-m

    Quick update for the sequencing runs.
    We were not really successful :-(

    In total, we did not get many reads:
    -259 failed reads (one mapping to: Naumovozyma castellii)
    -Kraken standard DB: 56 mapped to human
    -3 passed reads (one mapping to: Saccharomyces cerevisiae)

    Milad Miladi
    @mmiladi
    @teresa-m Could you please share the Galaxy history? Thanks.
    Two recent papers studying brewing yeast and their hybrids:
    Might be good for inspirational research-oriented ideas
    teresa-m
    @teresa-m
    https://usegalaxy.eu/u/teresa-m/h/latrappednasample3 Edit Share Url
    Milad Miladi
    @mmiladi
    Milad Miladi
    @mmiladi
    B. bruxellensis has a positive contribution to brewing of Belgium Lambic and Gueuze beers: https://twitter.com/jo_schacherer/status/1191469068181803008?s=21
    Milad Miladi
    @mmiladi
    nanopore for monitoring food outbreaks: https://twitter.com/cellstoshell/status/1199794575147180032
    Anika
    @erxleben
    hey
    did the WS take place today?
    teresa-m
    @teresa-m
    Next week. :-)
    Anika
    @erxleben
    Ahhh, true
    Milad Miladi
    @mmiladi
    IT requirements in case decided to buy a laptop specific for MinION nanopore:
    minion-it-reqs.pdf
    Having SSD storage and USB3 are some of the most importants.
    Bérénice Batut
    @bebatut
    the question is: do we really need so much resources? Teresa has 12GB RAM, i5 and small SSD
    Milad Miladi
    @mmiladi
    These are general recommendations. As long as only Beer is sequenced lower specs should suffice.