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

Liang Fang1,2,3, Guipeng Li1,2,3, Zhiyuan Sun2

  • 1Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.

Molecular Systems Biology
|April 6, 2021
PubMed
Summary

We developed a concanavalin A-based sample barcoding (CASB) strategy for cost-effective single-cell sequencing. CASB efficiently labels cells, accurately assigns them to samples, and detects doublets, preserving transcriptomic and epigenomic data.

Keywords:
CASBcombinatorial sample indexingsample multiplexingsingle-cell RNA sequencingsingle-nucleus ATAC sequencing

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Area of Science:

  • Single-cell genomics
  • Molecular biology
  • Biotechnology

Background:

  • Sample multiplexing is crucial for cost-effective single-cell sequencing.
  • Existing methods are limited in universality and cost-effectiveness.
  • Identifying artifacts like cell doublets is essential.

Purpose of the Study:

  • To develop a universal and cost-effective sample barcoding strategy for single-cell sequencing.
  • To introduce the concanavalin A-based sample barcoding (CASB) strategy.
  • To demonstrate CASB's applicability with both single-cell mRNA and ATAC sequencing.

Main Methods:

  • Developed a concanavalin A-based sample barcoding (CASB) strategy.
  • Applied CASB followed by single-cell RNA sequencing (scRNA-seq).
  • Integrated CASB with single-nucleus ATAC sequencing (snATAC-seq) and scRNA-seq.
  • Utilized combinatorial indexing with CASB.

Main Results:

  • CASB demonstrated high labeling efficiency and accuracy in cell/nuclei assignment across diverse cell types.
  • The method showed high sensitivity in detecting doublets.
  • CASB successfully tracked transcriptomic dynamics in drug-perturbed cancer cells, revealing heterogeneous responses.
  • CASB elucidated IFN-γ-mediated dynamic changes in epigenome and transcriptome, identifying key transcription factors.
  • Combinatorial indexing with CASB confirmed its high scalability.

Conclusions:

  • CASB is a versatile, cost-effective, and efficient method for sample multiplexing in single-cell genomics.
  • The strategy preserves transcriptomic and epigenomic patterns with minimal sample processing.
  • CASB enables deeper insights into cellular heterogeneity and dynamic biological processes.