Dataset Information

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.

ABSTRACT: 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)-? and perform eQTL analysis on 23 pooled samples.

SUBMITTER: Kang HM

PROVIDER: S-EPMC5784859 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Publications

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.

Kang Hyun Min HM Subramaniam Meena M Targ Sasha S Nguyen Michelle M Maliskova Lenka L McCarthy Elizabeth E Wan Eunice E Wong Simon S Byrnes Lauren L Lanata Cristina M CM Gate Rachel E RE Mostafavi Sara S Marson Alexander A Zaitlen Noah N Criswell Lindsey A LA Ye Chun Jimmie CJ

Nature biotechnology 20171211 1

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 c ...[more]

PMID: 29227470

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Dataset Information

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.

Publications

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.

Similar Datasets

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