CASB: a concanavalin A-based sample barcoding strategy for single-cell sequencing.
CASB: a concanavalin A-based sample barcoding strategy for single-cell sequencing.
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CASB：基于刀豆球蛋白 A 的单细胞测序样品条形码策略
DOI：
10.15252/msb.202010060
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发表时间：
2021-04
影响因子：
9.9
通讯作者：
Chen W
中科院分区：
文献类型：
--
作者：
Fang L;Li G;Sun Z;Zhu Q;Cui H;Li Y;Zhang J;Liang W;Wei W;Hu Y;Chen W
样品多路复用通过降低成本，揭示相似样品之间的细微差异，以及识别诸如细胞双峰之类的伪影，从而促进单细胞测序。然而，普遍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豆豆蛋白a的样本条形码策略（CASB），它可以被单细胞mRNA和ATAC（转座酶可及染色质测定）测序技术所遵循。该方法涉及最小的样品处理，从而保留完整的转录组或表观基因组模式。我们证明了它的高标记效率，无论细胞类型和遗传背景如何，都能准确地将细胞/细胞核分配到样品中，并且通过三种应用在检测双分子序列方面具有高灵敏度：1)CASB和scRNA - seq跟踪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异质性反应；2) CASB结合snATAC - seq和scRNA - seq，阐明了IFN - γ介导的表观基因组和转录组谱的动态变化，确定了IFN - γ异质性应答的转录因子；3) CASB组合索引，显示了其较高的可扩展性。CASB是一种兼容单细胞RNA - seq和ATAC - seq的样品多路复用新方法。CASB是高度准确，高效和敏感的，并允许更多不同类型的信息被纳入单细胞测序实验。
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. 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.
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影响因子：
64.8
作者：
Cao, Junyue;Spielmann, Malte;Shendure, Jay
通讯作者：
Shendure, Jay
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
单细胞染色质可及性揭示了调节变化的原理。
影响因子：
64.8
作者：
Buenrostro JD;Wu B;Litzenburger UM;Ruff D;Gonzales ML;Snyder MP;Chang HY;Greenleaf WJ
通讯作者：
Greenleaf WJ
影响因子：
64.8
作者：
Garnett, Mathew J.;Edelman, Elena J.;Heidorn, Sonja J.;Greenman, Chris D.;Dastur, Anahita;Lau, King Wai;Greninger, Patricia;Thompson, I. Richard;Luo, Xi;Soares, Jorge;Liu, Qingsong;Iorio, Francesco;Surdez, Didier;Chen, Li;Milano, Randy J.;Bignell, Graham R.;Tam, Ah T.;Davies, Helen;Stevenson, Jesse A.;Barthorpe, Syd;Lutz, Stephen R.;Kogera, Fiona;Lawrence, Karl;McLaren-Douglas, Anne;Mitropoulos, Xeni;Mironenko, Tatiana;Thi, Helen;Richardson, Laura;Zhou, Wenjun;Jewitt, Frances;Zhang, Tinghu;O'Brien, Patrick;Boisvert, Jessica L.;Price, Stacey;Hur, Wooyoung;Yang, Wanjuan;Deng, Xianming;Butler, Adam;Choi, Hwan Geun;Chang, JaeWon;Baselga, Jose;Stamenkovic, Ivan;Engelman, Jeffrey A.;Sharma, Sreenath V.;Delattre, Olivier;Saez-Rodriguez, Julio;Gray, Nathanael S.;Settleman, Jeffrey;Futreal, P. Andrew;Haber, Daniel A.;Stratton, Michael R.;Ramaswamy, Sridhar;McDermott, Ultan;Benes, Cyril H.
通讯作者：
Benes, Cyril H.
DOI：
10.1126/science.aau0730
发表时间：
2018-09-28
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Cao J;Cusanovich DA;Ramani V;Aghamirzaie D;Pliner HA;Hill AJ;Daza RM;McFaline-Figueroa JL;Packer JS;Christiansen L;Steemers FJ;Adey AC;Trapnell C;Shendure J
通讯作者：
Shendure J