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Construction of multiplexed transcriptome NGS libraries of microdissected tissue samples based on combinational DNA
Kaitong Dang1, Yue Zhao1, Kaiqiang Ye1
1State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China.
Biotechnology Journal
|October 11, 2023
Summary
We developed combinational DNA barcode (CDB)-seq, a cost-effective method for spatial transcriptomics. This technique enables medium-throughput transcriptome analysis of microdissected tissues, addressing limitations of current high-throughput methods.
Area of Science:
- Genomics
- Molecular Biology
- Biotechnology
Background:
- Spatial transcriptomics enables positional transcriptome analyses using single-cell RNA sequencing and microdissection.
- Current methods face challenges in throughput due to high costs and time demands, particularly at the single-cell level.
Purpose of the Study:
- To develop a medium-throughput, multiplexed approach for spatial transcriptome analysis of microdissected tissue samples.
- To address the limitations of existing high-throughput spatial transcriptomics techniques.
Main Methods:
- Proposed combinational DNA barcode (CDB)-seq, integrating Smart-3SEQ and CDB magnetic microbeads.
- Optimized CDB microbead preparation conditions and applied the method to various RNA extracts and tissue types (fresh frozen and FFPE mouse brain).
Main Results:
- Successfully obtained transcriptomic profiles from tens of microdissected samples using CDB-seq.
- Demonstrated a simple, cost-effective workflow for spatial transcriptome analysis.
Conclusions:
- CDB-seq offers a promising, accessible method for spatial transcriptomics.
- The technique facilitates medium-throughput analysis of microdissected tissues, expanding research capabilities.
