Merfish

Multiplexed Error-Robust Fluorescence in situ Hybridization

MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells.

  • Combinatorial Labeling
  • Sequential Imaging
  • Error Robust Barcoding

MERFISH Advantages

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High Spatial Resolution

Localize RNA transcripts with subcellular resolution.

High Throughput

Profile a square centimeter of tissue in a single run.

High Sensitivity

Detect difficult-to-characterize lowly expressed genes with single-molecule sensitivity.

High Multiplexing Power

Custom multiplexing from 100s of RNAs to transcriptome-scale.

Peer-Reviewed Publications

Deep profiling of the expression of RNAs in single cells in their native context with MERFISH has revealed cell type, state, organization, interactions, and function within cell culture and tissue.

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

Chenglong Xia, Jean Fan, George Emanuel, Junjie Hao, and Xiaowei Zhuang

PNAS 116, 19490-19499 (2019)

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Multiplexed detection of RNA using MERFISH and branched DNA amplification

Chenglong Xia, Hazen P. Babcock, Jeffrey R. Moffitt & Xiaowei Zhuang

Scientific Reports 9, 7721 (2019)

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Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

Jeffrey R. Moffitt, Dhananjay Bambah-Mukku, Stephen W. Eichhorn, Eric Vaughn, Karthik Shekhar, Julio D. Perez, Nimrod D. Rubinstein, Junjie Hao, Aviv Regev, Catherine Dulac, Xiaowei Zhuang

Science 362, 6416-eaau5324 (2018)

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Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy

Guiping Wang, Jeffrey R. Moffitt & Xiaowei Zhuang

Scientific Reports 8, 4847 (2018)

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High-Throughput, Image-Based Screening of Genetic Variant Libraries

George Emanuel, Jeffrey R. Moffitt & Xiaowei Zhuang

Nature Methods 14, 1159-1162 (2017)

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High-Performance Multiplexed Fluorescence in situ Hybridization in Culture and Tissue with Matrix Imprinting and Clearing

Jeffrey R. Moffitt, Junjie Hao, Dhananjay Bambah-Mukku, Tian Lu, Catherine Dulac, and Xiaowei Zhuang

PNAS 113, 14456-14461 (2016)

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High-Throughput Single-Cell Gene-Expression Profiling with Multiplexed Error-Robust Fluorescence in situ Hybridization

Jeffrey R. Moffitt, Junjie Hao, Guiping Wang, Kok Hao Chen, Hazen P. Babcock, and Xiaowei Zhuang

PNAS 113, 11046-11051 (2016)

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RNA Imaging with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH)

J.R.Moffitt, X.Zhuang

Methods in Enzymology 572, 1-49 (2016)

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Spatially resolved, highly multiplexed RNA profiling in single cells

Kok Hao Chen, Alistair N. Boettiger, Jeffrey R. Moffitt, Siyuan Wang, Xiaowei Zhuang

Science 348, aaa6090 (2015)

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If you are interested in applying MERFISH to your research, click here to learn more about Vizgen’s early engagement programs

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