FISH-based RNA detection in paraffin-embedded tissue can be challenging, with complicated procedures producing uncertain results and poor image quality. Here, we developed a robust RNA detection method based on graphene oxide (GO) quenching and recovery of fluorescence in situ hybridization (G-FISH) in formalin-fixed paraffin-embedded (FFPE) tissues. Using G-FISH technique, the long noncoding BC1 RNA, β -actin mRNA, miR-124a and miR-21 could be detected in the cytoplasm of a mouse brain, primary hippocampal neurons, and glioblastoma multiforme tumor tissues, respectively. G-FISH showed the increased BC1 RNA level in individual hippocampal neurons of Alzheimer's disease brain. The fluorescence recovered by G-FISH correlated highly with the amount of miR-21, as measured by real time RT-PCR. We propose G-FISH as a simple, fast, inexpensive, and sensitive method for RNA detection, with very low background, which could be applied to a variety of researches or diagnostic purposes.peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/143628 doi: bioRxiv preprint first posted online May. 29, 2017; Coding and noncoding RNA genes regulate cellular phenotypes distinctly in multicellular organisms, and their differential expression characterizes the phenotypes of individual cells in tissues, revealing significant spatial heterogeneity and complexity.Fluorescence in situ hybridization (FISH) methods enable the visualization of the subtleties of RNA expression that contributes to cellular developmental or pathological changes at the subcellular or organismal scales. Thus, FISH is used routinely to identify disease biomarkers using formalin fixed, paraffin embedded (FFPE) tissue specimens archived for future medical research after long-term storage [1,2] . Numerous efforts have been made to improve the image quality of in situ RNA detection, especially for microRNAs (miRNAs), as well as for mRNAs, at subcellular resolution [3][4][5] . However, the intricate and laborious conventional FISH methods for FFPE tissue sections and the concomitant poor image quality have prevented the easy determination of the expression signatures of RNA biomarkers of interest in clinical practice. Denaturation of fluorescence-labeled probes and off-target hybridization, even for such short molecules as miRNAs, lead to low sensitivity and high background with low specificity [6][7][8] . Herein, we propose a graphene oxide (GO) quenching-based method, termed G-FISH (GO quenching and recovery of fluorescence in situ hybridization) to overcome these shortcomings [9][10][11] . GO was used to quench fluorophores attached to nucleic acid probes and to deliver this fluorophore-labeled nucleic acid-GO complex into cells. This method is simpler and faster than the conventional FISH to detect various RNAs, such as long noncoding RNAs (lncRNAs), miRNAs, and mRNAs in FFPE tissue, as well as frozen tissue or live cells cultured in ...