Depositing half a billion beads

[pmiguel]

Version 3plus SOLiD runs call for slide densities around 500 million beads. The problem is that in our hands deposition efficiency is highly variable.

For our last slide we tried to calculate the number of beads to deposit based on our WFA. But while the WFA had 64% deposition efficiency, the actual run only gave us 50% efficiency.

Anyone have this issue solved? Or is not seeing it?

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Phillip

[snetmcom]

im not sure what you mean by deposition efficiency? is this a metric you have created?

bead deposition is still not linear. I get best results with 120% of my WFA numbers as with v3.

the WFA numbers are much more user dependant with v3plus it seems. If your deposition is off in some manner, it will scale up very poorly.

[pmiguel]

I believe that "deposition efficiency" is an Applied Biosystems term meaning percentage of bead counted in the focal map of a run divided by the number of beads added to the slide. Some of the beads do not stick, apparently.

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Phillip

[snetmcom]

yeah. never heard of that.
Not all of the beads stick, even more so when you are around 500 million. I have never had attrition post focal map though.

I have not had an issue hitting 450+ million with my calculations either. Maybe something is going wrong at 3' mod.

[pmiguel]

yeah. never heard of that.
Not all of the beads stick, even more so when you are around 500 million. I have never had attrition post focal map though.

I have not had an issue hitting 450+ million with my calculations either. Maybe something is going wrong at 3' mod.

No, we have not seen post focal map attrition either. We have returned to doing the 3' modification overnight.

We actually did get to 474 million loaded, but that required loading every bead that we had left. The efficiency was a little better than we got for the WFA--we had projected having less than 400 million.

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Phillip