Introduction to bioimaging‐based spatial multi‐omic novel methods

• Published in: Quantitative Biology
• Main Authors: Yan, Yan, Yang, Liheng, Meng, Leyuan, Su, Haochen, Zhou, Cheng, Yu, Le, Li, Zhengtu, Zhang, Xu, Cai, Huihua, Gao, Juntao
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2023
• Subjects: Applied Mathematics; Computer Science Applications; Biochemistry, Genetics and Molecular Biology (miscellaneous); Modeling and Simulation; Orca
• Online Access: http://dx.doi.org/10.15302/j-qb-023-0332; https://onlinelibrary.wiley.com/doi/pdf/10.15302/J-QB-023-0332

In this review, we introduced five different multiplex FISH methods used for image‐based spatial multi‐omics: seqFISH+, merFISH, DNA seqFISH+, DNA merFISH, and MINA. We provided a systematic collective perspective to review these FISH methods that could significantly benefit researchers on conducting their studies in the field. Our study provided an informative survey on these multiplex FISH methods. Therefore, this review would provide better understanding for researchers in the community to help them select the proper method, in order to understand the molecular mechanism in life sciences. Background Spatial multi‐omics are demonstrated to be a powerful method to assist researchers on genetic studies. In this review, bioimaging‐based spatial multi‐omics techniques such as seqFISH+, merFISH, integrated DNA seqFISH+, DNA merFISH, and MINA are introduced along with each technique’s probe design, development, and imaging processes. Results seqFISH employed 4–5 fluorophores to barcode and conducted multiple rounds of hybridization, in order that mRNA can be identified through color‐coding. seqFISH+ added 60 pseudo‐color and distributed them equally into three channels to enhance imaging power, in order that i.e. , 24,000 genes can be imaged in total. merFISH utilized 4 out 16 Hamming distance to innovatively provide a robust error‐detecting method. MINA, a methodology combining merFISH (multiplexed error‐robust fluorescence in situ hybridization) and chromosomal tracing, enabled multiplexed genomic architecture imaged in mammalian single cells. Optical reconstruction of chromatin architecture (ORCA) a method that could conduct DNA path tracing in nanoscale manner with kilobase resolution, an FISH variation that improved genetic resolution, enable high‐precision fiducial registration and sequential imaging, and utilized Oligopaint probe to hybridize the short genomic region ranging from 2 to 10 kilobase. ORCA then prescribes these short section primary probes with individual barcodes to attach fluorophore and to be ...