MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices
MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices
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DOI：
10.1038/s41592-019-0433-8
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发表时间：
2019-07-01
期刊：
影响因子：
48
通讯作者：
Gartner, Zev J.
中科院分区：
文献类型：
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作者：
McGinnistm, Christopher S.;Patterson, David M.;Gartner, Zev J.
样本复用通过降低成本和识别诸如细胞 doublets（可能指细胞双联体等异常情况，需结合更多背景确定准确含义）等人为因素促进了单细胞RNA测序（scRNA - seq）。然而，通用且可扩展的样本条形码策略尚未被描述。因此我们开发了MULTI - seq：一种使用脂质标记索引用于单细胞和单核RNA测序的复用方法。MULTI - seq试剂能够对任何具有可及质膜的物种的任何细胞类型或细胞核进行条形码标记。该方法涉及最少的样本处理，从而保留了细胞活力和内源基因表达模式。当使用MULTI - seq条形码丰度将细胞分类到样本组时，通过识别doublets以及恢复那些原本会被标准质量控制流程丢弃的低RNA含量细胞，数据质量得以提高。我们使用MULTI - seq追踪T细胞激活的动态，用原代人乳腺上皮细胞进行96重扰动实验，并对从三阴性乳腺癌患者来源的异种移植小鼠模型中分离出的冷冻保存的肿瘤和转移部位进行复用。
Sample multiplexing facilitates scRNA-seq by reducing costs and identifying artifacts such as cell doublets. However, universal and scalable sample barcoding strategies have not been described. We therefore developed MULTI-seq: multiplexing using lipid-tagged indices for single-cell and single-nucleus RNA sequencing. MULTI-seq reagents can barcode any cell type or nucleus from any species with an accessible plasma membrane. The method involves minimal sample processing, thereby preserving cell viability and endogenous gene expression patterns. When cells are classified into sample groups using MULTI-seq barcode abundances, data quality is improved through doublet identification and recovery of cells with low RNA content that would otherwise be discarded by standard quality-control workflows. We use MULTI-seq to track the dynamics of T-cell activation, perform a 96-plex perturbation experiment with primary human mammary epithelial cells and multiplex cryopreserved tumors and metastatic sites isolated from a patient-derived xenograft mouse model of triple-negative breast cancer.