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Multiplexed droplet single-cell RNA-sequencing using natural genetic variation
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Journal Article
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation
2018
Overview
Droplet single-cell RNA-seq is applied to large numbers of pooled samples from unrelated individuals.
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 droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). 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 single-nucleotide polymorphisms (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 eight 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 interferon (IFN)-β and perform eQTL analysis on 23 pooled samples.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
/ 45/91
/ 49/62
/ Biomedical Engineering/Biotechnology
/ Cells
/ Genetics
/ Genotype
/ High-Throughput Nucleotide Sequencing - methods
/ Humans
/ Interferons - therapeutic use
/ Lupus Erythematosus, Systemic - drug therapy
/ Lupus Erythematosus, Systemic - genetics
/ Polymorphism, Single Nucleotide - genetics
/ Quantitative Trait Loci - genetics
/ RNA
/ Single-Cell Analysis - methods
/ Single-nucleotide polymorphism
/ Software
