Yes, but specific FISH techniques must be applied. CARD-FISH and aldehyde fixation are NOT compatible with single cell genomics. Please apply regular (no signal amplification) FISH on either live or ethanol-fixed cells and then cryopreserve them using SCGC’s standard protocol. References for compatible FISH protocols:
Haroon MF, Skennerton CT, Steen JA, Lachner N, Hugenholtz P, Tyson GW (2013) In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery. Methods in Enzymology 531:3-19.
Yilmaz S, Haroon MF, Rabkin BA, Tyson GW, Hugenholtz P (2010) Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. The ISME Journal 4:1352-1356.