Sylwestrak, E.L. et al. Cell 164, 792–804 (2016).

Tissue-clearing approaches have made it possible to image deep inside tissues that are usually inaccessible because of light scattering. However, currently available protocols are optimized for the visualization of proteins. Sylwestrak et al. adapted the CLARITY clearing method to make it compatible with RNA in situ hybridization. The researchers included an additional fixation step in the procedure, which preserves RNA even for long-term sample storage, and found that DNA probes showed superior penetration compared to RNA probes. Amplification via the hairpin chain reaction resulted in high signal-to-noise ratios, especially for low-abundance transcripts. The modified CLARITY protocol is compatible with antibody labeling and preserves the fluorescence of expressed reporter proteins. The researchers demonstrated their method by detecting more than ten mRNA species and several microRNAs in mouse and human brain samples.