I have done many bacterial transformations over the past few years without any major problems.
I use NEB 5-alpha high efficiency cells for transformations with plasmids, according to the NEB protocol
But in the past 2 weeks, whenever I perform the outgrowth step with SOC medium, after the 1 hr incubation, the cells aggregate together in a lumpy mass in the tube. I have never noticed this before, using the same protocol I always use: For the SOC outgrowth step, I warm the SOC medium to 37oC and then add that to the cells that are incubating on ice after heat-shock.
I have tested this with NEB SOC and home-brew SOC and it occurred in both cases. The cells are also over 6 months old.
Could the pre-warmed SOC suddenly be causing this issue, or are the cells just old and expired?
Should I keep the SOC cold, to avoid further stress to the cells after the heat-shock?
I keep my SOC at room temperature. I've not seen any issues like you've described after adding to the heat-shocked cells.
Are you rocking/shaking the outgrowth culture during the 1 hour incubation? Do you get no colony growth after plating when you see the clump in your outgrowth culture? Have you tried plating right after adding the SOC (skipping the 1 hour incubation)?
what is the transformation efficiency?
I have the same clump situation sometimes, but the transformation efficiency is OK.
Are you getting uniform colonies after transformation? I had a cell clumping issue one time and it turned out the person who made the competent cells contaminated them with Staph aureus (they had a nasty cold when prepping the cells).
I usually use room temp SOC, that part should be fine.
Another possibility for the clumping is your shaker is set to a lower rate, allowing cells to settle.
Old cells that are less viable would only contribute a tiny amount of dead cells to the vial, that doesn't seem a likely source for clumps.
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