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Re: Any experiences with Geneamp 9700 cycler?
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Michael Sullivan
Apr 16, 2013, 12:50:31 PM4/16/13
to met...@magpie.bio.indiana.edu
We've had the 9700 (over 10 years) for quite some time (over 10 years) with no real problems. Are you using the little black tube insert for single tubes and the red one for strip tubes? Without those you will crush the tubes (but I think these are similar to what gets used with the 2700 (which we also have). I will admit that I haven't watched the temps closely for quite some time, but we're not having problems with our PCR either.
Mike
---
Michael L. Sullivan, PhD
Research Molecular Geneticist
US Dairy Forage Research Center
1925 Linden Drive
Madison, WI 53706
608-890-0046 (Phone)
608-890-0076 (FAX)
On Apr 15, 2013, at 11:10 PM, DK wrote:
> I got the unit used after >10 years of using PE 2700 with good and
> very consitent results. Was assuming that 9700 is going to be the
> same - just better. It's supposed to be the Casdillac of thermo
> cyclers, after all.
>
> Well, the thing warps my tubes (dome-capped) badly so that
> opening them after the cycling is a real physical challenge. Maybe
> related to that crazy 104C heated cover temperature that I cannot
> seem to change. It also seems to overshoot by a second or two
> at every temprerature (95C is momentarily 96.5 and 55 is actually
> 53.4 for good two seconds).
>
> All in all, the thing seems really inferior to its smaller and less
> expensive cousin. Am I doing something wrong?
>
> DK
> _______________________________________________
> Methods mailing list
> Met...@net.bio.net
> http://www.bio.net/biomail/listinfo/methods
Mike
---
Michael L. Sullivan, PhD
Research Molecular Geneticist
US Dairy Forage Research Center
1925 Linden Drive
Madison, WI 53706
608-890-0046 (Phone)
608-890-0076 (FAX)
On Apr 15, 2013, at 11:10 PM, DK wrote:
> I got the unit used after >10 years of using PE 2700 with good and
> very consitent results. Was assuming that 9700 is going to be the
> same - just better. It's supposed to be the Casdillac of thermo
> cyclers, after all.
>
> Well, the thing warps my tubes (dome-capped) badly so that
> opening them after the cycling is a real physical challenge. Maybe
> related to that crazy 104C heated cover temperature that I cannot
> seem to change. It also seems to overshoot by a second or two
> at every temprerature (95C is momentarily 96.5 and 55 is actually
> 53.4 for good two seconds).
>
> All in all, the thing seems really inferior to its smaller and less
> expensive cousin. Am I doing something wrong?
>
> DK
> _______________________________________________
> Methods mailing list
> Met...@net.bio.net
> http://www.bio.net/biomail/listinfo/methods
Duncan Clark
Apr 18, 2013, 5:00:42 AM4/18/13
to
Historians believe that in newspost
<mailman.265.136613...@net.bio.net> on Tue, 16 Apr 2013,
Michael Sullivan <mlsu...@wisc.edu> penned the following literary
masterpiece:
Only issues we have had are one board failure and a block failure. No
issues with the heated lid affecting tubes.
104C is pretty standard for a heated lid.
DK how are you determining overshoot, measurement by thermocouple in a
tube or watching the temp. The displayed temp is block temp and not tube
temp which, will always lag behind.
Duncan
--
I love deadlines. I especially like the whooshing noise they make as
they go flying by.
Duncan Clark
GeneSys Ltd.
<mailman.265.136613...@net.bio.net> on Tue, 16 Apr 2013,
Michael Sullivan <mlsu...@wisc.edu> penned the following literary
masterpiece:
>We've had the 9700 (over 10 years) for quite some time (over 10 years) with no real problems.
Likewise we have two over at least that period.
Only issues we have had are one board failure and a block failure. No
issues with the heated lid affecting tubes.
104C is pretty standard for a heated lid.
DK how are you determining overshoot, measurement by thermocouple in a
tube or watching the temp. The displayed temp is block temp and not tube
temp which, will always lag behind.
Duncan
--
I love deadlines. I especially like the whooshing noise they make as
they go flying by.
Duncan Clark
GeneSys Ltd.
Message has been deleted
Duncan Clark
Apr 19, 2013, 11:23:14 AM4/19/13
to
Historians believe that in newspost <kkq6h5$ilf$1...@dont-email.me> on Fri,
19 Apr 2013, DK <d...@no.email.thankstospam.net> penned the following
literary masterpiece:
>Another opinion, perfectly
>reasonable, is that the kind of tubes one uses really matters.
>What tubes do you use? I used the ones that worked really well
>on 2720 model and I don't think that they are made of polypropylene,
>for example. PE/ABI claim that plasticware requirements for 9700
>and 2700 series are identical. My problem stems from the fact that
>this is most definitely not the case. (Or I am having a bad dream).
We use what used to be ABgene tubes, now part of Thermofisher.
>
>>104C is pretty standard for a heated lid.
>
>Really? I thought 100C is the standard. But I really don't have experience
>with that many cyclers. Good to know it's not a fundamental problem.
It's not going to really matter. Polypropylene melts a long way above
that so anything approx. will do.
>
>>DK how are you determining overshoot, measurement by thermocouple in a
>>tube or watching the temp. The displayed temp is block temp and not tube
>>temp which, will always lag behind.
>
>In the initial testing, I stuck a thermocouple wire betwen a block and a
>thin-walled tube jammed in place. *Looked* accurate enough and
>of course I am not about to buy $2000 calibration kit (which just might
>to be the same thing...)
The problem with the thermocouple is that it will be measuring block
temperature and not the in tube temperature. There will be at least a
0.5C difference. Just as difficult measuring in the tube because the
sheer mass of even a tiny thermocouple will pull heat out of the small
volume in the tube.
A multiplex PCR across all wells and run out on an agarose gel is pretty
good at testing consistency across a block. Overshoot or undershoot
isn't usually too much of an issue providing it is consistent across the
whole block. I don't want a PCR working in the middle of a block and
failing at all the edges!
19 Apr 2013, DK <d...@no.email.thankstospam.net> penned the following
literary masterpiece:
>Another opinion, perfectly
>reasonable, is that the kind of tubes one uses really matters.
>What tubes do you use? I used the ones that worked really well
>on 2720 model and I don't think that they are made of polypropylene,
>for example. PE/ABI claim that plasticware requirements for 9700
>and 2700 series are identical. My problem stems from the fact that
>this is most definitely not the case. (Or I am having a bad dream).
We use what used to be ABgene tubes, now part of Thermofisher.
>
>>104C is pretty standard for a heated lid.
>
>with that many cyclers. Good to know it's not a fundamental problem.
It's not going to really matter. Polypropylene melts a long way above
that so anything approx. will do.
>
>>DK how are you determining overshoot, measurement by thermocouple in a
>>tube or watching the temp. The displayed temp is block temp and not tube
>>temp which, will always lag behind.
>
>thin-walled tube jammed in place. *Looked* accurate enough and
>of course I am not about to buy $2000 calibration kit (which just might
>to be the same thing...)
The problem with the thermocouple is that it will be measuring block
temperature and not the in tube temperature. There will be at least a
0.5C difference. Just as difficult measuring in the tube because the
sheer mass of even a tiny thermocouple will pull heat out of the small
volume in the tube.
A multiplex PCR across all wells and run out on an agarose gel is pretty
good at testing consistency across a block. Overshoot or undershoot
isn't usually too much of an issue providing it is consistent across the
whole block. I don't want a PCR working in the middle of a block and
failing at all the edges!
Christian Praetorius
Apr 20, 2013, 4:31:46 PM4/20/13
to
d...@no.email.thankstospam.net (DK) wrote:
>Following Mike's advise, I ordered some of the PE's original "trays"
We have been using four of the 9700s with these "trays" for years now
without any problems.
Christian
--
X-no-Sig: yes
>Following Mike's advise, I ordered some of the PE's original "trays"
We have been using four of the 9700s with these "trays" for years now
without any problems.
Christian
--
X-no-Sig: yes
Message has been deleted
Michael Sullivan
Apr 26, 2013, 12:01:13 PM4/26/13
to met...@magpie.bio.indiana.edu
Yeah, I haven't quite figured out why they designed it this way, although the tube holder is sort of nice for working with the strip tubes. I don't think there's a way to adjust how much pressure the lid applies (like the MJ DNA engine [now biorad?] has), so maybe ABI's approach with the 9700 was to just apply a lot of pressure and have a device to keep the tubes from being crushed?
My experience with the 9700 was rather like yours, I think. When we first got it, I crushed a bunch of tubes, because who consults the manual for how to put tubes into a PCR machine? :)
I initially thought that since I was not using the ABI tubes, that was the problem. So once I bought the ABI tubes and crushed some of those, I realized there must be something wrong.
I think maybe the 2720 applies less pressure from the lid than the 9700.... at least that's how it feels to me, so that's probably why you were able to use it without crushing your tubes.
Anyway, I'm glad you have that problem fixed!
Mike
---
Michael L. Sullivan, PhD
Research Molecular Geneticist
US Dairy Forage Research Center
1925 Linden Drive
Madison, WI 53706
608-890-0046 (Phone)
608-890-0076 (FAX)
On Apr 25, 2013, at 10:39 PM, DK wrote:
> In article <atgc9j...@mid.individual.net>, Christian Praetorius <pr...@gmx.net> wrote:
>> d...@no.email.thankstospam.net (DK) wrote:
>>
>>> Following Mike's advise, I ordered some of the PE's original "trays"
>>
>> We have been using four of the 9700s with these "trays" for years now
>> without any problems.
>
> Now that I've got the trays, I have no problems too. It just puzzles me
> that while 2720 and 9700 formally list the same requirements for
> plasticware, 2720 is prefectly usable without any trays who 9700
> is not.
>
> Bad design, IMO.
My experience with the 9700 was rather like yours, I think. When we first got it, I crushed a bunch of tubes, because who consults the manual for how to put tubes into a PCR machine? :)
I initially thought that since I was not using the ABI tubes, that was the problem. So once I bought the ABI tubes and crushed some of those, I realized there must be something wrong.
I think maybe the 2720 applies less pressure from the lid than the 9700.... at least that's how it feels to me, so that's probably why you were able to use it without crushing your tubes.
Anyway, I'm glad you have that problem fixed!
Mike
---
Michael L. Sullivan, PhD
Research Molecular Geneticist
US Dairy Forage Research Center
1925 Linden Drive
Madison, WI 53706
608-890-0046 (Phone)
608-890-0076 (FAX)
> In article <atgc9j...@mid.individual.net>, Christian Praetorius <pr...@gmx.net> wrote:
>> d...@no.email.thankstospam.net (DK) wrote:
>>
>>> Following Mike's advise, I ordered some of the PE's original "trays"
>>
>> We have been using four of the 9700s with these "trays" for years now
>> without any problems.
>
> that while 2720 and 9700 formally list the same requirements for
> plasticware, 2720 is prefectly usable without any trays who 9700
> is not.
>
> Bad design, IMO.
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