I have bubbles on my well plate and I think to remove using the hose and glass pipette same as we aspirate exhausted medium. I know I shall touch the wall of well but don't know why bubbles happened.
If the problem is bubbles at the surface of the liquid in the wells, you may be able to pop them by blowing a gentle stream of ethanol (or methanol) vapor over them from a laboratory squirt bottle, the kind with a straw that connects to the cap, containing a little ethanol in the bottom and with the straw removed. This method can be used when there are bubbles in many wells. If there are just a few wells with bubbles, you can pop them with a pipet tip, using a fresh tip for each bubble.
One reason bubbles get into the wells is that they are expelled from the pipet tip used to fill the wells because some of the liquid sticks to the tip, so air is blown out instead of liquid. To avoid this problem, fill and empty the tips with the liquid at least once to coat them before dispensing into the wells. Or use an electronic pipettor that allows you to fill the tip with more liquid than you are going to dispense.
You are possibly using hydrogel culture media. To avoid bubbles within the hydrogel, it would be advisable to use distilled ― or otherwise boiled water ― and to avoid aeration by swirling during liquor (or sol) agitation, prior to gelation. Alternatively or complementary, you could apply sonication followed by partial vacuum. If UV or gamma irradiation is being considered to sterilize the hydrogel, it seems preferable not irradiate the sol, but rather the gel, kept well below the gel―sol transition temperature.
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