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Old 06-08-2012, 06:19 AM   #1
Gorbenzer
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Default Chip reutilization, anyone tried or have any suggestion?

Hi everyone,
on the net i've read of some people utilizing Chip two times... after the first PGM run they wash the chip, spin it upside down and then utilize it for another PGM run.

Anyone tried?
Should not be so expensive, expecially with 314 chips that require the use of just half the library.
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Old 06-08-2012, 06:49 AM   #2
diagen
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What exactly are the factors preventing such re-usage? Do beads get stack in the wells, or wells get damaged, or sensors do not respond properly?
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Old 06-08-2012, 09:34 AM   #3
IonTorrent
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Quote:
Originally Posted by diagen View Post
What exactly are the factors preventing such re-usage? Do beads get stack in the wells, or wells get damaged, or sensors do not respond properly?
Hi Gorbenzer and diagen,

In our experience it is not possible to reuse the chip for a new sample and achieve the expected performance. This is based both on internal work and what has been reported by PGM customers who have tried to do this on their own. In fact, it is extremely difficult to dislodge the Ion Sphere Particles once they are loaded in the wells. There is also no assurance that the sensors would perform as designed if the chips are handled otherwise than as recommended.
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Old 06-08-2012, 10:33 AM   #4
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Quote:
Originally Posted by IonTorrent View Post
Hi Gorbenzer and diagen,

In our experience it is not possible to reuse the chip for a new sample and achieve the expected performance. This is based both on internal work and what has been reported by PGM customers who have tried to do this on their own. In fact, it is extremely difficult to dislodge the Ion Sphere Particles once they are loaded in the wells. There is also no assurance that the sensors would perform as designed if the chips are handled otherwise than as recommended.
For those who feel they can't trust Ion Torrent's answer due to their 'financial conflict of interest', I'd just like to throw in my two cents:

I can't say for sure as I've never tried this with an Ion Torrent chip, but I helped developed Illumina's original bead array platform and I can say that it was extremely difficult to remove the beads once they were in the wells. Sonication did the best, but the results weren't consistent (and the treatment often damaged the chip surface). Ion Torrent has done a pretty good job of reducing the prices on their older chips, so I think you're really better off not reusing them.
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Old 06-08-2012, 12:57 PM   #5
diagen
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I hope the definite opinion from experts will not block user's creativity. One just should try various conditions to release the beads. Surface interaction forces may be masked by high salt and ionic detergents, or simply by organic dissolvents.
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Old 06-08-2012, 04:01 PM   #6
scbaker
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Well, I wouldn't call myself an expert (although I did have the help of some really good surface chemists). But by all means, please be as creative as you can and try everything. Also, be sure to report back any successes or failures so we can all learn. But when it comes to generating data for a 'real' project, I'm not sure I'd think it would be worth the $100 savings to reuse a 314 chip (but I guess it depends on the nature of the experiment). Good luck and let us know how it goes!
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Old 06-30-2012, 12:07 PM   #7
genseq
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Cool

http://seqanswers.com/forums/showthread.php?t=18451
"We've got som odd results with PE. Seems that we are loosing lots of beads during washings of the chip after finishing the first run. Has anybody encountered anything similar?"
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Old 07-03-2012, 02:27 PM   #8
snetmcom
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Quote:
Originally Posted by genseq View Post
http://seqanswers.com/forums/showthread.php?t=18451
"We've got som odd results with PE. Seems that we are loosing lots of beads during washings of the chip after finishing the first run. Has anybody encountered anything similar?"
the beads aren't actually washing out of the chip. this has been detailed somewhere on the community i think. something to do with polymerase in the detection of live wells.

Unless you can remove 90% of the wells, i just don't see the value in this.
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Old 03-15-2016, 09:30 PM   #9
kroggen
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Hi everyone!

Any news on this topic?

Any success with washing and reuse?

I am willing to try it
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Old 04-13-2016, 01:53 AM   #10
Markiyan
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What about some enzymatic treatment with proteases/etc? (test on beads under the microscope for digestion) for finding optimal conditions...
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Old 08-12-2016, 05:05 AM   #11
Smoki
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Quote:
Originally Posted by kroggen View Post
Hi everyone!

Any news on this topic?

Any success with washing and reuse?

I am willing to try it
The latest protocols from Ion Torrent even involve spinning the loaded chip upside down in the centrifuge. So my bet is that it is virtually impossible to dislodge and remove the spheres for a second run.
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Old 08-12-2016, 06:33 AM   #12
genseq
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What about 0,1M NaOH?
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Old 10-14-2016, 09:33 AM   #13
genseq
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Default Reincarnation


https://ioncommunity.thermofisher.co...ge/49993#49993
thomas.gross
I come from a smaller lab and like most ion users there is some learning with the PGM machine. I have successfully re-ran 10 to 15 318chips. If you have a bad OT2 run and don't really want to toss it and you know there will be extra reagent on the PGM then try this. I pipette ~100ul H20 up and down 5 times, then spin upside down for 10 seconds and repeat this 3 times. If I am going to store the chip I fill it with H20 then parafilm it tight. I have used chips a up to month old. Mode 1 (PCR GBS)is new 318 1st run, Then rinse and spin 3x then put back on PGM for finish the back side of reagents. 75% loading (PCR GBS) then 73% (RAD GBS). IF more questions, I will post more. This was HI-Q View PGM and OT2 Same 318 chip.
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Old 02-07-2017, 01:43 PM   #14
mlirski
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Default Concerning PI chips...

Since our lab had some old (v2) sequencing reagents left and the v2 chip is no longer sold, I was looking for a way to reuse some chips from recent runs. Unfortunately I wasn't able to remove the beads from the wells. I tried dessicating them with isopropanol, sonicating, washing away with detergents (Trition X-100 / SDS) and boiling them out by immersing the chip in water and applying quick vacuum, all with no luck.
To monitor the chip loading I stained the beads with DAPI and used fluorescence microscope to excitate the stain. From my observations the beads fit tightly in the wells and there is also a DNA layer, which can make a difference in the micrometer scale.
I planned to try DNase digestion, but found another solution.
I took a chip, that was barely loaded - the beads were lost prior to chip loading. It was laying in the cabinet for almost 2 years, so I expected total failure. I washed and prepared chip as if it was a new chip, then loaded it and...
I got 90% loading, and good quality reads! I compared the results with replicates sequenced the usual way and found no batch effect, almost perfect correlation. I was quite surprised, given the chip storage time and the fact that it looked bad - it had cracked cristals of salt from dried W2 buffer in the middle, and yet it worked just fine. Silicon will never cease to amaze me...
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Old 06-09-2017, 11:18 AM   #15
genseq
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Default Chip Washin Station

https://www.youtube.com/watch?v=eojg02AUAxw
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Old 06-12-2017, 01:38 AM   #16
mlirski
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Default In english?

Is there an answer to the thread in the lecture? I know russian a bit but I don't want to listen for half hour and find nothing new...
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Old 08-01-2017, 01:36 AM   #17
genseq
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Russian again. Sorry.
https://geektimes.ru/post/291613/
https://www.slideshare.net/MailRuGroup/diy-75130226
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Old 08-04-2017, 12:09 PM   #18
Marcela Astete
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Default Can I load the Ion Torrent chip and use it the next day?

Can I load the Ion Torrent chip and use it the next day?
Thank you
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Old 08-05-2017, 09:11 AM   #19
BioHak
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Quote:
Originally Posted by Marcela Astete View Post
Can I load the Ion Torrent chip and use it the next day?
Thank you
In my experience you can save the chip at 4C over the weekend and room temp overnight and not see significant difference in results
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