Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections

Xinbin Tang; Jiayu Chen; Xinya Zhang; Xuzhu Liu; Zhaoxiang Xie; Kaipeng Wei; Jianlong Qiu; Weiyan Ma; Chen Lin; Rongqin Ke

doi:10.1016/j.jgg.2023.02.004

Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections

doi: 10.1016/j.jgg.2023.02.004

a. School of Medicine and School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, China;
b. Department of Pathology, The 910 Hospital, Quanzhou, Fujian 362000, China

基金项目:

This study was supported by the Natural Science Foundation of Fujian Province (2022J06022), the Quanzhou Science and Technology Plan Project (2021C040R), and the Scientific Research Funds of Huaqiao University.

详细信息

通讯作者:
Chen Lin,E-mail:chen.lin@hqu.edu.cn

Rongqin Ke,E-mail:rke@hqu.edu.cn

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- 文章访问数: 298
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出版历程
- 收稿日期: 2022-11-03
- 录用日期: 2023-02-02
- 修回日期: 2023-01-30
- 刊出日期: 2023-02-15

Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections

a. School of Medicine and School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, China;
b. Department of Pathology, The 910 Hospital, Quanzhou, Fujian 362000, China

Funds:

摘要

摘要: Spatial transcriptomics enables the study of localization-indexed gene expression activity in tissues, providing the transcriptional landscape that in turn indicates the potential regulatory networks of gene expression. In situ sequencing (ISS) is a targeted spatial transcriptomic technique, based on padlock probe and rolling circle amplification combined with next-generation sequencing chemistry, for highly multiplexed in situ gene expression profiling. Here, we present improved in situ sequencing (IISS) that exploits a new probing and barcoding approach, combined with advanced image analysis pipelines for high-resolution targeted spatial gene expression profiling. We develop an improved combinatorial probe anchor ligation chemistry using a 2-base encoding strategy for barcode interrogation. The new encoding strategy results in higher signal intensity as well as improved specificity for in situ sequencing, while maintaining a streamlined analysis pipeline for targeted spatial transcriptomics. We show that IISS can be applied to both fresh frozen tissue and formalin-fixed paraffin-embedded tissue sections for single-cell level spatial gene expression analysis, based on which the developmental trajectory and cell-cell communication networks can also be constructed.
- Spatial transcriptomics /
- In situ sequencing /
- Single cell /
- Gene expression profiling /
- Imaging
Abstract: Spatial transcriptomics enables the study of localization-indexed gene expression activity in tissues, providing the transcriptional landscape that in turn indicates the potential regulatory networks of gene expression. In situ sequencing (ISS) is a targeted spatial transcriptomic technique, based on padlock probe and rolling circle amplification combined with next-generation sequencing chemistry, for highly multiplexed in situ gene expression profiling. Here, we present improved in situ sequencing (IISS) that exploits a new probing and barcoding approach, combined with advanced image analysis pipelines for high-resolution targeted spatial gene expression profiling. We develop an improved combinatorial probe anchor ligation chemistry using a 2-base encoding strategy for barcode interrogation. The new encoding strategy results in higher signal intensity as well as improved specificity for in situ sequencing, while maintaining a streamlined analysis pipeline for targeted spatial transcriptomics. We show that IISS can be applied to both fresh frozen tissue and formalin-fixed paraffin-embedded tissue sections for single-cell level spatial gene expression analysis, based on which the developmental trajectory and cell-cell communication networks can also be constructed.
- Spatial transcriptomics /
- In situ sequencing /
- Single cell /
- Gene expression profiling /
- Imaging

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参考文献(33)

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Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections

doi: 10.1016/j.jgg.2023.02.004

通讯作者:
Chen Lin,E-mail:chen.lin@hqu.edu.cn

Rongqin Ke,E-mail:rke@hqu.edu.cn

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Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections

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留言板

Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections

doi: 10.1016/j.jgg.2023.02.004

通讯作者: Chen Lin,E-mail:chen.lin@hqu.edu.cn Rongqin Ke,E-mail:rke@hqu.edu.cn

计量

出版历程

Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections

计量

出版历程

目录

通讯作者:
Chen Lin,E-mail:chen.lin@hqu.edu.cn

Rongqin Ke,E-mail:rke@hqu.edu.cn