Clean room or not?

denice_please · 05-15-2012, 05:36 PM

Hello everyone! We're setting up a sequencing core facility, and the floor plan and room layout are quite challenging. First of all, do we need to have a clean room? We're going to be working with a MiSeq, an Ion PGM and a 3730xl. Some labs are HEPA-filtered but I've also seen some that are not. Any feedback on this?

Second, do we need a separate room for sample prep or say a separate PCR room? Or can I just have them all in one room and have the equipment that will be used together on one long benchtop? Or maybe have them all in one room but each equipment and peripherals have their own bencthop?

Any feedback would be appreciated!

KYR · 05-20-2012, 10:24 PM

Your sequencer should have its own room in a particle-free area, with a private door and / or double door to enter. The temperature of the room shouldn't be over 20 or 25 .. I'm not sure about that one, but it is temperature sensitive for sure. And the temperature shouldn't vary either. No human movement, no drink , nothing inside, only the NGS operator should be allowed to get in.

PCR rooms should be separated as well. Many would tell you that PCR machines don't need to be in a private room, in our lab we do a lot of PCR, RT-PCR and etc.. it is true that it works well at room temperature but all those appliances are temperature SENSITIVE, means that the less it vary, the longer you will have it with you and less defect/troubles you will encounter.

Sample prep can be done at RT, as long as it is not done in the same room as your sequencer.

So to review : PCR / NGS / Sample prep ==> 3 different rooms, temperature sensitive, RT okay for Sample prep, not okay for NGS & PCR.

james hadfield · 05-21-2012, 02:45 AM

All the NGS providers have install spec sheets that are probably worth your asking for, just email their TechSupport desks.

Ilumina require a stable temperature within a range, but stability is the most important factor. Ideally a separate air-con and heating system to the rest of the building.

I'd recommend careful attention to pre and post-amplification areas. There is a lot of PCR involved in library prep and some systems add bacrodes via PCR. Any contamination wil be difficult to identify if it happens. Preferably you'ld have two tooms and perhaps a hood in one of them as well.

I'd disagree a little with KYR. We allow loads of people into our NGS room so we can show it off. Sometimes the sequencers even get on the TV!

I'd agree about separating library prep and NGS. You might end up doing al your post-PCR in the same rom as your NGS though. The more rooms you get the smaller they are in most places. A hood is almost as good as a separate room and this allows larger rooms and a nicer working environment.

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05-15-2012, 05:36 PM	#1
denice_please Junior Member Location: Philippines Join Date: May 2012 Posts: 3	Clean room or not? Hello everyone! We're setting up a sequencing core facility, and the floor plan and room layout are quite challenging. First of all, do we need to have a clean room? We're going to be working with a MiSeq, an Ion PGM and a 3730xl. Some labs are HEPA-filtered but I've also seen some that are not. Any feedback on this? Second, do we need a separate room for sample prep or say a separate PCR room? Or can I just have them all in one room and have the equipment that will be used together on one long benchtop? Or maybe have them all in one room but each equipment and peripherals have their own bencthop? Any feedback would be appreciated!

05-20-2012, 10:24 PM	#2
KYR Member Location: Toronto Join Date: May 2012 Posts: 18	Your sequencer should have its own room in a particle-free area, with a private door and / or double door to enter. The temperature of the room shouldn't be over 20 or 25 .. I'm not sure about that one, but it is temperature sensitive for sure. And the temperature shouldn't vary either. No human movement, no drink , nothing inside, only the NGS operator should be allowed to get in. PCR rooms should be separated as well. Many would tell you that PCR machines don't need to be in a private room, in our lab we do a lot of PCR, RT-PCR and etc.. it is true that it works well at room temperature but all those appliances are temperature SENSITIVE, means that the less it vary, the longer you will have it with you and less defect/troubles you will encounter. Sample prep can be done at RT, as long as it is not done in the same room as your sequencer. So to review : PCR / NGS / Sample prep ==> 3 different rooms, temperature sensitive, RT okay for Sample prep, not okay for NGS & PCR.

05-21-2012, 02:45 AM	#3
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	All the NGS providers have install spec sheets that are probably worth your asking for, just email their TechSupport desks. Ilumina require a stable temperature within a range, but stability is the most important factor. Ideally a separate air-con and heating system to the rest of the building. I'd recommend careful attention to pre and post-amplification areas. There is a lot of PCR involved in library prep and some systems add bacrodes via PCR. Any contamination wil be difficult to identify if it happens. Preferably you'ld have two tooms and perhaps a hood in one of them as well. I'd disagree a little with KYR. We allow loads of people into our NGS room so we can show it off. Sometimes the sequencers even get on the TV! I'd agree about separating library prep and NGS. You might end up doing al your post-PCR in the same rom as your NGS though. The more rooms you get the smaller they are in most places. A hood is almost as good as a separate room and this allows larger rooms and a nicer working environment.