<Noxz>
looked more into biohacking.. likely going the bio-listic/gene gun route for knocking out genes in a few things I am interested in, vs, say, CRISPR
<Noxz>
making the micropore detector cheaper would be nice, though $1k USD to get started into it is not bad
<Noxz>
(minION)
<SpeedEvil>
1K for the basic thingy, you need more to be able to sample stuff
<Noxz>
they give you two plates of pore detector thingies
<Noxz>
for the 1k
<Noxz>
and you can rinse/reuse them a bit
<Noxz>
but, yeah, you need to have other equip, that's just a small sequencer
<SpeedEvil>
i mean to go from a biological sample to DNA in a form suitable to sequence
<Noxz>
extracting DNA isnt too difficult, that's a middle school afternoon project
<Noxz>
I'd love to explore cheaper alternatives, but it isnt too bad for something that works
pie_ has quit [Ping timeout: 248 seconds]
<SpeedEvil>
Extracting it in nice shape to sample, with little contaminating DNA, on the other hand
<Noxz>
I think you also need to segment it a bit for sequencing.. that the proteine based micropores can straighten up some dna, but not a scomplete strand
<Noxz>
random segmentations, that then your ocmputer/cloud has to compare and rejoin it all
<nmz787>
Noxz: I don't think you can rinse/reuse the pores... they give 512 (nano) pores per cell/thingy... and only expect about 2/3 of them will work for decent amount of time... and they stop working during a run
<nmz787>
at least from people who've used them @home
<nmz787>
DNA extraction can take between 10 and 30 mins usually
<Noxz>
Sebastian Cocioba says you can rinse them, sure a somewhat short lifespan, but more than just one run
<nmz787>
that's who I was quoting actually :)
<nmz787>
so I guess he would know
<Noxz>
I am going off more from talks he has done, I havent really read anything he's written
<Noxz>
yet
<Noxz>
I need to
<nmz787>
segmenting the DNA isn't required actually
<nmz787>
the minION gives two protocols
<nmz787>
one with segmenting, one without
<nmz787>
ah, he's my facebook friend
<nmz787>
so we've had random messages
<nmz787>
'quick, I need to check some possible bullshit'
<Noxz>
my fb profile was for raves/music event info, mainly, and I quit it a few months back
<Noxz>
I may rejoin it later, but I have other stuff to occupy my time with
<Noxz>
it wasnt under my real name, so highly unprofessional
<nmz787>
they will not produce the longest DNA, like a gentler digestive technique combined with magnetic bead isolation
<nmz787>
nah, he doesn't seem to use IRC
<nmz787>
he uses that one that all the millenials use though
<nmz787>
slack I think
<Noxz>
we use slack internally at work
<Noxz>
and I am somewhat aware of these sort of filter vials from my brief intro into bio
<nmz787>
he invited me into it when I signed on to his Patreon thing... but that was mainly to get some lab manual he was working on... so I didn't really hang out there
<nmz787>
those columns basically have silica in them, and come with a few different salt solutions of various concentrations
<nmz787>
the salt content changes the affinity between DNA and silica
<Noxz>
right
<nmz787>
so you rinse the cell extract through the column, the DNA binds, you rinse non-bound stuff away, then change collection tubes and rinse with diff salt concentration and the DNA elutes
<Noxz>
right
<Noxz>
but yeah, good link for inexpensive ones, I bookmarked
<nmz787>
I think they sell the solutions separately too... so you could just buy those and I could send you some columns
<nmz787>
I have a box of 50 that I've only used 1 or 2 of since buying earlier this year
<Noxz>
welp, lemme finish the house, rebuild the chemlab, then I'll get into bio more
<nmz787>
:)
<Noxz>
there's a few things I want to do, but initially mainly gene knockout
<nmz787>
story of my life, pretty much
<nmz787>
have you seen the howto for making a gene gun?
<Noxz>
for purpose on all if them I write 'graphene research'
<Noxz>
yeah, that one is on youtube
<Noxz>
there was like 3 or so people with them easily found on yt
<nmz787>
cool
<Noxz>
enough that I got the gist
<nmz787>
I have been focusing on actually making the DNA, been glad others have kept working on delivery :)
<Noxz>
and is more applicable for various organisms, over crispr
<nmz787>
I started my biotech B.S. 10 years ago this month :O
<Noxz>
do you order primers? are are you making them?
<nmz787>
I don't think I really realized DNA synthesis was the major bottleneck for another year or two
<nmz787>
nah, I am actually working on the polymer synthesis level
<nmz787>
hoping to see the day when either my efforts or others will achieve million/billion times cheaper synthesis
<nmz787>
so I can actually use these tools like I do computer compilers (where I often have lots of typos and compile errors)
<Noxz>
$50-120 for a 60 AA length primer isnt too bad
<Noxz>
for some general purpose
<Noxz>
sure, $250 to test one gene knockout isnt too cheap
<Noxz>
but if it's all I want to do?
<nmz787>
I had grand ideas originally for actually doing stuff with new/funky/remixed DNA... but got stuck when I realized my ideas would cost millions in synthesis and other lab work
<nmz787>
nah, most interesting things are more than 1 or 2 enzymes/genes/regulators
<nmz787>
when you get to 10 genes, you're basically in a money-pit
<Noxz>
my initial test case will be knockout/in
<nmz787>
yeah knockout is simple
<nmz787>
my original motivator was thinking if only we could add an oil pump into the side/wall of a high oil content algae... we could just grow it and skim the top of a pond for oil for biofuel use
<Noxz>
from recent reads, will flank the gene in question w/ 40 AA pairs, and then the knockin gene w/ 20 or so, using a 60 lenght primer, *2 for both ends, and you PCR the knockin/repalcement/nulld gene with it to get the dna you want to transfect
<nmz787>
good old homologous recombination
<Noxz>
and then some mutagensis will form, yeah
<Noxz>
that is likely the route I will be looking into, first
<Noxz>
w/ a gene gun
<Noxz>
but I still want to sequence the strains I have on hand
<Noxz>
the issue of ordering some known standard is always going to be 'difficult' to get for hobbyists
<nmz787>
do you know the-odin.com ?
<nmz787>
also, 16S rRNA sequencing shouldn't be too much
<nmz787>
for strain barcoding
<Noxz>
yeah
<Noxz>
I wish I got into this stuff when I still lieved in the bay area
<Noxz>
would have visited the guy who runs it
<Noxz>
Josiah Zayner
<Noxz>
I will likely get some stuff from him, like the PCR and centrifuge and such
<nmz787>
I stayed at the-odin for a night the last time I was down there ~2 months ago
<nmz787>
seemed like a reasonable operation
<Noxz>
does he have a day job or is that it currently?
<nmz787>
that's it from what I know
<nmz787>
he is also a facebook friend
<Noxz>
yeah, I figured that too ;)
<nmz787>
saw yesterday they have hundreds of thousands in revenue
<Noxz>
I may make a fb account for my science stuff once I get the lab atleast ready to be built again
<Noxz>
oh wow
<Noxz>
few videos of the ktis in use on yt, so it kinda made me ??