Tweet
Humidity causes imaging issues!
Note added 7/23/2010:
Turns out the phenomenon described below was not caused by ambient humidity, but instead by a cracked slide in the adjacent flowcell. The crack is was not visible -- or at least I did not see it when I looked -- until today.
I was told by ABI that imaging is performed at 25 oC, so humidity is not going to be an issue unless you run your SOLiD in a swamp or a steam room.
End of note
----------------------------------
Just a heads up for those who, like us, don't live in a desert and have less than perfect climate control:
beware humidity!
We have been plagued by intermittent "black panels" where no data can be collected. By "intermittent", I mean, a panel will be black one cycle, but okay the next. Lots of possible causes for such an issue, but here is one that you may not have thought of.
The culprit was the high humidity in our lab, courtesy of our mid-western US summers. The slides apparently are a little cooler than ambient, so moisture condenses on the imaging surface. The result is:
or
If you double click on a black panel in ICS you will see something like:
or follow this link to see a larger image:
blurry.png
Note that the focal map shows the beads all clearly focused, but the post ligation imaging shows distorted images. I mistook them for some sort of vibration artifact at first.
Finally the condensation got so bad, I knew I would have to, at least, repeat the primer, so we paused the run and I pulled down the flow cell to take a look at the slide. I thought the problem might be bubbles in the flow cell. Instead I saw hundreds of tiny beads of water condensed on the outside surface of the slide. Here is what the flowcell looked like (the one on the left):
I gently wiped the surface off and continued the scanning. The black panels mostly disappeared.
But next time the slide chills a little, they will be back. I have to get the humidity down in the lab. Specifications Applied Biosystems provide call for <80% humidity, "non-condensing".
--
Phillip
Turns out the phenomenon described below was not caused by ambient humidity, but instead by a cracked slide in the adjacent flowcell. The crack is was not visible -- or at least I did not see it when I looked -- until today.
I was told by ABI that imaging is performed at 25 oC, so humidity is not going to be an issue unless you run your SOLiD in a swamp or a steam room.
End of note
----------------------------------
Just a heads up for those who, like us, don't live in a desert and have less than perfect climate control:
beware humidity!
We have been plagued by intermittent "black panels" where no data can be collected. By "intermittent", I mean, a panel will be black one cycle, but okay the next. Lots of possible causes for such an issue, but here is one that you may not have thought of.
The culprit was the high humidity in our lab, courtesy of our mid-western US summers. The slides apparently are a little cooler than ambient, so moisture condenses on the imaging surface. The result is:
or
If you double click on a black panel in ICS you will see something like:
or follow this link to see a larger image:
blurry.png
Note that the focal map shows the beads all clearly focused, but the post ligation imaging shows distorted images. I mistook them for some sort of vibration artifact at first.
Finally the condensation got so bad, I knew I would have to, at least, repeat the primer, so we paused the run and I pulled down the flow cell to take a look at the slide. I thought the problem might be bubbles in the flow cell. Instead I saw hundreds of tiny beads of water condensed on the outside surface of the slide. Here is what the flowcell looked like (the one on the left):
I gently wiped the surface off and continued the scanning. The black panels mostly disappeared.
But next time the slide chills a little, they will be back. I have to get the humidity down in the lab. Specifications Applied Biosystems provide call for <80% humidity, "non-condensing".
--
Phillip
Comment