CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing
Abstract 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 sampl...
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doaj-ebc718c2af1444ad82d6c34afa66d1322021-08-02T22:11:48ZengWileyMolecular Systems Biology1744-42922021-04-01174n/an/a10.15252/msb.202010060CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencingLiang Fang0Guipeng Li1Zhiyuan Sun2Qionghua Zhu3Huanhuan Cui4Yunfei Li5Jingwen Zhang6Weizheng Liang7Wencheng Wei8Yuhui Hu9Wei Chen10Shenzhen Key Laboratory of Gene Regulation and Systems Biology School of Life Sciences Southern University of Science and Technology Shenzhen ChinaShenzhen Key Laboratory of Gene Regulation and Systems Biology School of Life Sciences Southern University of Science and Technology Shenzhen ChinaDepartment of Biology School of Life Sciences Southern University of Science and Technology Shenzhen ChinaShenzhen Key Laboratory of Gene Regulation and Systems Biology School of Life Sciences Southern University of Science and Technology Shenzhen ChinaShenzhen Key Laboratory of Gene Regulation and Systems Biology School of Life Sciences Southern University of Science and Technology Shenzhen ChinaDepartment of Biology School of Life Sciences Southern University of Science and Technology Shenzhen ChinaDepartment of Biology School of Life Sciences Southern University of Science and Technology Shenzhen ChinaDepartment of Biology School of Life Sciences Southern University of Science and Technology Shenzhen ChinaDepartment of Biology School of Life Sciences Southern University of Science and Technology Shenzhen ChinaShenzhen Key Laboratory of Gene Regulation and Systems Biology School of Life Sciences Southern University of Science and Technology Shenzhen ChinaShenzhen Key Laboratory of Gene Regulation and Systems Biology School of Life Sciences Southern University of Science and Technology Shenzhen ChinaAbstract 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.https://doi.org/10.15252/msb.202010060CASBcombinatorial sample indexingsample multiplexingsingle‐cell RNA sequencingsingle‐nucleus ATAC sequencing |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Liang Fang Guipeng Li Zhiyuan Sun Qionghua Zhu Huanhuan Cui Yunfei Li Jingwen Zhang Weizheng Liang Wencheng Wei Yuhui Hu Wei Chen |
spellingShingle |
Liang Fang Guipeng Li Zhiyuan Sun Qionghua Zhu Huanhuan Cui Yunfei Li Jingwen Zhang Weizheng Liang Wencheng Wei Yuhui Hu Wei Chen CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing Molecular Systems Biology CASB combinatorial sample indexing sample multiplexing single‐cell RNA sequencing single‐nucleus ATAC sequencing |
author_facet |
Liang Fang Guipeng Li Zhiyuan Sun Qionghua Zhu Huanhuan Cui Yunfei Li Jingwen Zhang Weizheng Liang Wencheng Wei Yuhui Hu Wei Chen |
author_sort |
Liang Fang |
title |
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing |
title_short |
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing |
title_full |
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing |
title_fullStr |
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing |
title_full_unstemmed |
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing |
title_sort |
casb: a concanavalin a‐based sample barcoding strategy for single‐cell sequencing |
publisher |
Wiley |
series |
Molecular Systems Biology |
issn |
1744-4292 |
publishDate |
2021-04-01 |
description |
Abstract 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. |
topic |
CASB combinatorial sample indexing sample multiplexing single‐cell RNA sequencing single‐nucleus ATAC sequencing |
url |
https://doi.org/10.15252/msb.202010060 |
work_keys_str_mv |
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