Multi-slice spatial transcriptome domain analysis with SpaDo

Bin Duan; Shaoqi Chen; Xiaojie Cheng; Qi Liu

doi:10.1186/s13059-024-03213-x

Multi-slice spatial transcriptome domain analysis with SpaDo

Genome Biol. 2024 Mar 19;25(1):73. doi: 10.1186/s13059-024-03213-x.

Authors

Bin Duan^#^{1

2

3

4}, Shaoqi Chen^#^{5

6

7

8}, Xiaojie Cheng^#^{5

6

7

8}, Qi Liu^{9

10

11

12}

Affiliations

¹ State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China. bioinfo_db@tongji.edu.cn.
² Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China. bioinfo_db@tongji.edu.cn.
³ Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201804, China. bioinfo_db@tongji.edu.cn.
⁴ Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China. bioinfo_db@tongji.edu.cn.
⁵ State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
⁶ Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
⁷ Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201804, China.
⁸ Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
⁹ State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China. qiliu@tongji.edu.cn.
¹⁰ Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China. qiliu@tongji.edu.cn.
¹¹ Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201804, China. qiliu@tongji.edu.cn.
¹² Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China. qiliu@tongji.edu.cn.

^# Contributed equally.

Abstract

With the rapid advancements in spatial transcriptome sequencing, multiple tissue slices are now available, enabling the integration and interpretation of spatial cellular landscapes. Herein, we introduce SpaDo, a tool for multi-slice spatial domain analysis, including modules for multi-slice spatial domain detection, reference-based annotation, and multiple slice clustering at both single-cell and spot resolutions. We demonstrate SpaDo's effectiveness with over 40 multi-slice spatial transcriptome datasets from 7 sequencing platforms. Our findings highlight SpaDo's potential to reveal novel biological insights in multi-slice spatial transcriptomes.

Keywords: Multiple slice analysis; Spatial domain detection; Spatial transcriptomics.

MeSH terms

Cluster Analysis
Gene Expression Profiling*
Single-Cell Analysis
Spatial Analysis
Transcriptome*

Abstract

MeSH terms

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