Journal article

Genotype-free demultiplexing of pooled single-cell RNA-seq

Jun Xu, Caitlin Falconer, Quan Nguyen, Joanna Crawford, Brett McKinnon, Sally Mortlock, Alice Pébay, Alex Hewitt, Anne Senabouth, Stacey Andersen, Nathan Palpant, Han Sheng Chiu, Grant Montgomery, Joseph Powell, Lachlan Coin

BMC | Published : 2019

Abstract

A variety of experimental and computational methods have been developed to demultiplex samples from pooled individuals in a single-cell RNA sequencing (scRNA-Seq) experiment which either require adding information (such as hashtag barcodes) or measuring information (such as genotypes) prior to pooling. We introduce scSplit which utilises genetic differences inferred from scRNA-Seq data alone to demultiplex pooled samples. scSplit also extracts a minimal set of high confidence presence/absence genotypes in each cluster which can be used to map clusters to original samples. Using a range of simulated, merged individual-sample as well as pooled multi-individual scRNA-Seq datasets, we show that ..

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Funding Acknowledgements

National Health and Medical Research Council Career Development Fellowship (LC, APP1130084; JP, APP1107599) National Health and Medical Research Council (JP, APP1143163 LC, APP1149029) Practitioner Fellowship (AWH) Senior Research Fellowship (AP), 1154389 Australian Research Council Future Fellowship (AP, FT140100047) Australian Research Council Discovery Project (JP, DP180101405) Stem Cells Australia -the Australian Research Council Special Research Initiative in Stem Cell Science (JP, AWH, AP, NP) Australian Research Council Development Early Career Researcher (QN, DE190100116)

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