Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
Mol Syst Biol. 2021 Apr;17(4):e10060. doi: 10.15252/msb.202010060.
Sample multiplexing facilitates single-cell sequencing by reducing costs, revealing subtle difference between similar samples, and identifying artifacts such as cell doublets. However, universal and cost-effective strategies are rather limited. Here, we reported a concanavalin A-based sample barcoding strategy (CASB), which could be followed by both single-cell mRNA and ATAC (assay for transposase-accessible chromatin) sequencing techniques. The method involves minimal sample processing, thereby preserving intact transcriptomic or epigenomic patterns. We demonstrated its high labeling efficiency, high accuracy in assigning cells/nuclei to samples regardless of cell type and genetic background, and high sensitivity in detecting doublets by three applications: 1) CASB followed by scRNA-seq to track the transcriptomic dynamics of a cancer cell line perturbed by multiple drugs, which revealed compound-specific heterogeneous response; 2) CASB together with both snATAC-seq and scRNA-seq to illustrate the IFN-γ-mediated dynamic changes on epigenome and transcriptome profile, which identified the transcription factor underlying heterogeneous IFN-γ response; and 3) combinatorial indexing by CASB, which demonstrated its high scalability.
样本多重化通过降低成本、揭示相似样本之间的细微差异以及识别细胞双联体等假象，促进了单细胞测序。然而，通用且具有成本效益的策略相当有限。在这里，我们报道了一种基于伴刀豆球蛋白 A 的样本条形码策略 (CASB)，它可以与单细胞 mRNA 和 ATAC（转座酶可及染色质分析）测序技术相结合。该方法涉及最小的样本处理，从而保持完整的转录组或表观基因组模式。我们通过三个应用证明了其高标记效率、无论细胞类型和遗传背景都能准确地将细胞/核分配到样本的能力，以及高灵敏度检测双联体的能力：1）CASB 后接单细胞 RNA-seq 跟踪受多种药物干扰的癌细胞系的转录组动力学，揭示了化合物特异性的异质性反应；2）CASB 与 snATAC-seq 和单细胞 RNA-seq 相结合，说明 IFN-γ 介导的表观基因组和转录组谱动态变化，确定了异质性 IFN-γ 反应背后的转录因子；3）通过 CASB 进行组合索引，证明了其高可扩展性。
