1) For each slide to be stripped, prepare 50 ml of 1% SDS (1.25 ml 20% SDS + 48.75 ml H2O). One 50 ml conical tube is used to strip one chip.
2) Warm 1% SDS to 60¾C.
3) Put slides into 50 ml tube containing prewarmed 1% SDS.
4) Incubate at 60¾C for 20 to 30 minutes in a rotating hybridization oven.
5) Wash chip in 6 X SSPE + 0.05% Triton-X by dipping chip into a 50 ml conical tube containing 6 X SSPE + 0.05% Triton-X. I usually dip the chip in slowly and remove it from the solution slowly. Dip the chip in 3-5 times. Dipping is done using forceps.
6) Dip slides into a 50 ml conical tube containing 0.06 X SSPE a few times.
7) During the last wash, slowly remove the chip from 0.06 X SSPE.

Comments:
Hybridized chips have to be stripped immediately or within 24 hours. If the hybridized chip is stored for a few days, it is VERY difficult or IMPOSSIBLE to remove all Cy3 channel signals from the chip. Stripping can also be performed in 2% SDS.