Protocol for Identification and Removal of Doublets with DoubletDecon

Erica A K DePasquale; Daniel Schnell; Kashish Chetal; Nathan Salomonis

doi:10.1016/j.xpro.2020.100085

Protocol for Identification and Removal of Doublets with DoubletDecon

STAR Protoc. 2020 Aug 11;1(2):100085. doi: 10.1016/j.xpro.2020.100085. eCollection 2020 Sep 18.

Authors

Erica A K DePasquale^{1

2}, Daniel Schnell^{1

3}, Kashish Chetal¹, Nathan Salomonis^{1

2

4}

Affiliations

¹ Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
² Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45221, USA.
³ Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
⁴ Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA.

Abstract

Retention of multiplet captures in single-cell RNA sequencing (scRNA-seq) data can hinder identification of discrete or transitional cell populations and associated marker genes. To overcome this challenge, we created DoubletDecon to identify and remove doublets, multiplets of two cells, by using a combination of deconvolution to identify putative doublets and analyses of unique gene expression. Here, we provide the protocol for running DoubletDecon on scRNA-seq data. For complete details on the use and execution of this protocol, please refer to DePasquale et al. (2019).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Exome Sequencing
Gene Expression / genetics
Gene Expression Profiling / methods*
Sequence Analysis, DNA / methods
Sequence Analysis, RNA / methods*
Single-Cell Analysis / methods*
Software

Grants and funding

R01 CA226802/CA/NCI NIH HHS/United States