Journal article

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

Jun Xu, Caitlin Falconer, Quan Nguyen, Joanna Crawford, Brett D McKinnon, Sally Mortlock, Anne Senabouth, Stacey Andersen, Han Sheng Chiu, Longda Jiang, Nathan J Palpant, Jian Yang, Michael D Mueller, Alex W Hewitt, Alice Pebay, Grant W Montgomery, Joseph E Powell, Lachlan JM Coin

Genome Biology | BMC | Published : 2019

Abstract

A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior to pooling. We introduce scSplit which utilizes genetic differences inferred from scRNA-seq data alone to demultiplex pooled samples. scSplit also enables mapping clusters to original samples. Using simulated, merged, and pooled multi-individual datasets, we show that scSplit prediction is highly concordant with demuxlet predictions and is highly consistent with the known truth in cell-hashing dataset. scSplit is ideally suited to samples without external genotype information and is available at: https://..

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Grants

Awarded by National Health and Medical Research Council


Awarded by Australian Research Council


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)