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Old 09-06-2013, 07:50 AM   #1
Location: Tucson, AZ, USA

Join Date: Oct 2010
Posts: 22
Default How about the learning curve?

Hi, all-

Happy Friday! I'm here looking for some advice from MiSeq owners.

I just received grant funding and am planning to purchase a MiSeq as part of the project plan. Previous to this, I’ve always sent libraries out for sequencing, but I have a decent non hands-on understanding of the rest of the process. I also have a good pipeline for dealing with the data once it comes off the sequencer, and I basically only sequence one type of library.

The company I work for is very small, so basically it’s going to be me and probably a tech learning how to use the sequencer. My boss (based in Boston) is very keen to hire a tech who has MiSeq experience, sparing us the learning curve. I (based in Tucson) am less sanguine about the chances of finding someone with that skill set here! So I’m here to ask for advice from people who have gone through the “new MiSeq” learning curve. How much time did it take you to get the hang of going from library to results? Any tips on making it easier? How about number of amazingly destroyed flow cells? Once a protocol is established, is it something I could train a fairly novice (but eager to learn) tech on?

I am also in the process of setting up my sequencing space, so any “I wish I had known…”s about workspace would also be much appreciated.

Thank you for your time!
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Old 09-06-2013, 08:06 AM   #2
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Location: Boston,MA

Join Date: Nov 2008
Posts: 122

The MiSeq is incredibly easy to run. The software (Experiment Manager)takes some getting used to but that can be done without risking samples. There are different selcetions that work with one kind of prep but not another (ie Nextera) taht you will have to figure out, but that is all ahead of sample loading.

The FAS for your area will train you and that is probably all you will need in terms of physical training. There is a help menu with videos built in to the software so you can always click and get a refresher on anything.

The only things I recommend is to be sure it is near an internet port so you can run base space, and have a keyboard accesible. There is a bit of typing to set up the run (depending on how many samples) and the touch screen can get annoying.
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Old 09-06-2013, 09:41 AM   #3
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Location: New England

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Actually running the MiSeq is dead easy. Anyone who can pipette and follow basic instructions can do it. Plus the FAS spends a couple of days with you and helps you set up a control run. The tricky part is making a good library and it sounds like you can already do that.

ETA: The MiSeq is really noisy with the fan blowing all the time (we were told to never turn it off, just wash it once a week to keep the fluidics clean). I wish it wasn't set up next to my desk. We also had to put a divider behind it so it wasn't blowing across the lab bench opposite it.
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Old 09-06-2013, 09:42 AM   #4
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Location: Oklahoma

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Everything is so kitted and cartridged out that if you can't run it I'm afraid there's very little hope for you in a wet lab. Making the libraries themselves is a far more intricate process than running the Miseq. The reagent cartridge even has a big orange arrow on it that says "put your libraries in this well".

The Miseq: So easy to run a PI could do it.

(PS: qPCR, qPCR, qPCR for quantification. Use the KAPA kit)
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Old 09-06-2013, 09:51 AM   #5
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Location: East Coast USA

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Have you decided on a plan as to how you want to handle the data? Will the data be shipped back to Boston (over the network/physical media)? Being in a company you may not be able to use basespace (which is a cloud based infrastructure that is not HIPAA compliant AFAIK).

MiSeq has a single ethernet port. If you ever need Illumina tech support to be able to log-in/diagnose any runs remotely it will have to be put on a proxy/open internet for a short time.

While running, a MiSeq can be pretty loud (cooling fans) so do not plan to put it next to your work bench (edit: I see that Microgirl123 has already pointed this out in her post).

You would also want to invest in a good UPS (something like a APC 2200XL or equivalent is great) in case local power supply is unreliable/not clean.

Buy a USB hub and/or a couple of USB extension cables (and a compact USB keyboard) so you are not fumbling with the USB ports on the back of the instrument all the time. There is only one easily accessible USB port on the front of the instrument.

MiSeq runs a full version of Win 7 (64-bit) OS so it otherwise behaves like a normal PC. Illumina does not recommend running an anti-virus program so you will want to keep it isolated from local network/internet.

Last edited by GenoMax; 09-06-2013 at 10:06 AM.
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Old 09-06-2013, 12:08 PM   #6
Location: Tucson, AZ, USA

Join Date: Oct 2010
Posts: 22

Awesome, that was exactly what I wanted to know. Thank you for such speedy replies.

@microgirl123: Fortunately, a loud fan will be okay, I'm getting our old "tissue culture room" - which, to my knowledge, no-one has ever done any tissue culture IN - to put the new machine in.

@GW_OK: already have the Kapa kit on order, and I LOVE your line about the ease of use.

@GenoMax: The setup tips are great. I just went to talk to our ordering person about a UPS. I plan to deal with the data's a form of targeted sequencing, so the data distills down to fairly small files. My boss would prefer to see a little table, not a huge bunch of fastq files!

thanks again, happy weekend-

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Old 09-06-2013, 12:24 PM   #7
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Location: Halifax, Nova Scotia

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Another reason why you wouldn't want your MiSeq in a space/on a bench that is used a lot is that it is sensitive to vibration.
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Old 09-09-2013, 04:40 AM   #8
Location: Portugal

Join Date: Apr 2011
Posts: 50

Hello everyone,

Yes its a bit noisy, "my" MiSeq was installed 2 meters from me.
We kept the machine off, when its not sequencing, and every Monday's we do a maintenance wash. When we have sample to load, we proceed first with a maintenance wash and sometimes a flow test, just to be sure that everything is OK.

I have plugged a keyboard, a mouse and a LCD (the other thing its to small!)
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Old 08-12-2014, 07:56 AM   #9
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Location: Denver

Join Date: Aug 2014
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I second JackieBadger's comment. I used to be in a lab that had a MiSeq, and the bench was in physical contact with a neighboring bench that had a frequently-used vortexer. We actually had an important screw work its way loose and prevent proper focusing!
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