Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.
复制标题
使用自然遗传变异的多重液滴单细胞RNA序列。
DOI：
10.1038/nbt.4042
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发表时间：
2018-01
影响因子：
46.9
通讯作者：
Ye CJ
中科院分区：
文献类型：
--
作者：
Kang HM;Subramaniam M;Targ S;Nguyen M;Maliskova L;McCarthy E;Wan E;Wong S;Byrnes L;Lanata CM;Gate RE;Mostafavi S;Marson A;Zaitlen N;Criswell LA;Ye CJ
液滴单细胞RNA测序（dscRNA-seq）已经实现了转录组的快速，大规模并行分析。然而，评估多个个体之间的差异表达受到低效样品处理和技术批量效应的阻碍。在这里，我们描述了一种计算工具，demuxlet，利用自然的遗传变异来确定每个细胞的样本身份，并检测含有两个细胞的液滴。这些功能使多重dscRNA-seq实验成为可能，其中来自不相关个体的细胞被合并并以比标准工作流程更高的通量捕获。使用模拟数据，我们表明，每个细胞50个SNP足以分配97%的单重峰，并在多达64个个体的池中识别92%的双重峰。给定8个合并样品中每一个的基因分型数据，demuxlet正确地恢复了>99%的单重峰的样品同一性，并以与先前估计一致的速率鉴定了双重峰。我们应用demuxlet来评估用IFN-β治疗的8个合并的狼疮患者样品中基因表达的细胞类型特异性变化，并对23个合并的样品进行eQTL分析。
Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each cell and detect droplets containing two cells. These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows. Using simulated data, we show that 50 SNPs per cell are sufficient to assign 97% of singlets and identify 92% of doublets in pools of up to 64 individuals. Given genotyping data for each of 8 pooled samples, demuxlet correctly recovers the sample identity of >99% of singlets and identifies doublets at rates consistent with previous estimates. We apply demuxlet to assess cell type-specific changes in gene expression in 8 pooled lupus patient samples treated with IFN-β and perform eQTL analysis on 23 pooled samples.
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