Int J Biol Sci 2020; 16(14):2663-2674. doi:10.7150/ijbs.43887

Research Paper

Encoding Method of Single-cell Spatial Transcriptomics Sequencing

Ying Zhou1, Erteng Jia1, Min Pan2, Xiangwei Zhao1, Qinyu Ge1✉

1. State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
2. School of Medicine, Southeast University, Nanjing 210097, China.

This is an open access article distributed under the terms of the Creative Commons Attribution License ( See for full terms and conditions.
Zhou Y, Jia E, Pan M, Zhao X, Ge Q. Encoding Method of Single-cell Spatial Transcriptomics Sequencing. Int J Biol Sci 2020; 16(14):2663-2674. doi:10.7150/ijbs.43887. Available from

File import instruction


Despite significant advances in parallel single-cell RNA sequencing revealing astonishing cellular heterogeneity in many tissue types, the spatial information in the tissue context remains missing. Spatial transcriptome sequencing technology is designed to distinguish the gene expression of individual cells in their original location. The technology is important for the identification of tissue function, tracking developmental processes, and pathological and molecular detection. Encoding the position information is the key to spatial transcriptomics because different methods have different encoding efficiencies and application scenarios. In this review, we focus on the latest technologies of single-cell spatial transcriptomics, including technologies based on microwell plates, barcoded bead arrays, microdissection, in situ hybridization, and barcode in situ targeting, as well as mixed separation-based technologies. Moreover, we compare these encoding methods for use as a reference when choosing the appropriate technology.

Keywords: Single-cell RNA sequencing, Spatial transcriptomics, Encoding method, In situ sequencing