I noticed in the FISSEQ protocol (http://www.sciencemag.org/content/343/6177/1360.long) fixed cells are treated with hydrochloric acid after they have already been permeabilized with ethanol or Triton-X100. What is the purpose of this?
They use HCl because they are "unmasking" antigenic sites using pepsin digestion. Pepsin is a potent protease that only works in an acidic environment. The idea is that the pepsin will degrade away protein complexes that may be masking antigens or mRNAs from antibodies or hybridizing oligos.