Details

Autor(en) / Beteiligte

• Fang, Liang
• Li, Guipeng
• Sun, Zhiyuan
• Zhu, Qionghua
• Cui, Huanhuan
• Li, Yunfei
• Zhang, Jingwen
• Liang, Weizheng
• Wei, Wencheng
• Hu, Yuhui
• Chen, Wei

Titel

CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing

Ist Teil von

• Molecular systems biology, 2021-04, Vol.17 (4), p.e10060-n/a

Ort / Verlag

England: John Wiley & Sons, Inc

Erscheinungsjahr

2021

Link zum Volltext

Quelle

Wiley Online Library - AutoHoldings Journals

Beschreibungen/Notizen

• 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. Synopsis CASB is a new method for sample multiplexing compatible with both single‐cell RNA‐seq and ATAC‐seq. CASB is highly accurate, efficient and sensitive and allows more diverse types of information to be incorporated in single‐cell sequencing experiments. CASB is the first single‐cell/nucleus sample multiplexing strategy compatible with both scRNA‐seq & snATAC‐seq. CASB allows both simultaneous combinatorial barcoding and sequential split‐pool barcoding. While being highly efficient, accurate and sensitive, CASB is experiment‐friendly and cost‐effective. CASB is a new method for sample multiplexing compatible with both single‐cell RNA‐seq and ATAC‐seq. CASB is highly accurate, efficient and sensitive and allows more diverse types of information to be incorporated in single‐cell sequencing experiments.