Multiplexed error-robust fluorescence in situ hybridization (MERFISH) is a massively parallelized form of the single-molecule fluorescence in situ hybridization (smFISH) method that can image and identify hundreds to thousands of different RNA species simultaneously.
Imaging based technologies or methods for the study of single-cell transcriptomes have now become very popular. These methods are commonly used as complementary techniques to single-cell RNA sequencing methods. The notion here is that quantitative measurements of the copy number and spatial distribution of fractions of the transcriptome in single cells will revolutionize our understanding of cell and tissue behavior. This knowledge may allow medical researchers to distinguish between healthy and diseased cells and tissues.
Single-molecule fluorescence in situ hybridization (smFISH) is an approach were individual RNAs are labeled using fluorescent probes. If imaging of these species is done in their native context, both copy number, and spatial context can be observed. Moffit et al. developed a technique called multiplexed error-robust fluorescence in situ hybridization (MERFISH) to achieve a higher throughput. This massively parallelized form of smFISH can image and identify hundreds to thousands of different RNA species simultaneously. The use of readout probes allows identification of large numbers of RNAs within a single sample via imaging.
In 2016, Moffit et al. reported that their advancements led to a dramatic increase in throughput using MERFISH. The researchers increased the throughput of MERFISH by two orders of magnitude. Improvements of MERFISH were made using multicolor imaging in combination with the use of chemical cleavage instead of photobleaching. This approach allowed removal of fluorescent signals between rounds of smFISH imaging thereby increasing the imaging field of view.
Using this improved approach the scientists were able to profile 130 RNAs across 40 mm2 of the sample containing approximately 39,000 human cells.
Reference
Jeffrey R. Moffitt, Junjie Hao, Guiping Wang, Kok Hao Chen, Hazen P. Babcock, and Xiaowei Zhuang; High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. PNAS 2016 : 1612826113v1-201612826.
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