Ga2x bubble problem

[Santosh]

We have a very strange problem with the GA2X machine here. We spotted few bubbles while doing the leak check with the actual reagents after placing the flow cell. The bubbles were found in the inlet pipe pumping reagents into the Flow cell, within the flow cell and also in the syringes that pump the fluids out of the machine. We do not know how the buubles found their way into the pipes and syringes. We always make sure that the reagent bottles are kept filled all the time. An engineer had visited the lab recently and could not conclude on how the bubbles were introduced into the system and neither could he solve our bubble problem. Instead, he suggested us to start wth the run. After the run started, we found that in each lane, there were few tiles which were black, instead of being either blue, green or yelow. I could make out quite clearly that it was a bubble issue. Does anyone here wrking on a same kind of machine, ever had a similar problem? If ye, I would be very grateful to that person if he or she could suggest me a solution.

SANTOSH

[Efortier]

Hi,

We have a GAIIx and experience the same bubbles as you describe during the leak check. Here is what I found. If you see the bubbles coming from the 'intake tube' (before reaching the front manifold) the bubbles are not related to leaks in the system, at leat for us. What happens is that if the reagent used for the leak test (PR2) is shaken vigorously and still cold when loaded on the GAIIx, microbubbles will get disolved in the reagent. When that cold reagent is pumped through the lines, it will warm up slightly and the microbubbles will expand and create bigger bubbles. For us this doesn't impact the run performance. But now I make sure that the PR1, PR2 and PR3 reagents are sitting at room temp without shaking for a few minutes.

If you want to be sure there is no leak in the system you can procede with the leak test using room temp water on a used flowcell after a post-run wash recipe. You should not see any bubbles. If you do see bubbles, then there is something wrong.

Hope this helps,

[Santosh]

Hey there, Thanq very much for a very prompt reply. What u say, actually makes a lot of sense to me. We have actually done a leak test using PW1 kept at the room temperature. But we never have shaken any of these vigorously before loading them on to the GA2X. Even then, we have seen this problem and now, unfortunately we have a bad run and I think it attributes to the bubbles which we had never seen earlier. What about u??? Do the bubbles persist in ur GA2X syringes or in the inlet pipe??? If they do, how seriously do you take them? Are they seen in every run you perform???

[Efortier]

Hi,

We usually don't get bad tiles during a run so I don't think the bubbles are a problem past the first cycle. Of course during a run I cannot open the instrument door and and watch for bubbles during the chemistry cycles. If you are getting a bad run due to this problem I would have your instrument checked again.

If you look at the pictures taken during the run can you see the bubbles?