title: Classification of low quality cells from single-cell RNA-seq data.
abstract: Single-cell RNA sequencing (scRNA-seq) has broad applications across biomedical research. One of the key challenges is to ensure that only single, live cells are included in downstream analysis, as the inclusion of compromised cells inevitably affects data interpretation. Here, we present a generic approach for processing scRNA-seq data and detecting low quality cells, using a curated set of over 20 biological and technical features. Our approach improves classification accuracy by over 30 % compared to traditional methods when tested on over 5,000 cells, including CD4+ T cells, bone marrow dendritic cells, and mouse embryonic stem cells.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. ti243@cam.ac.uk.|Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. ti243@cam.ac.uk.
authors.forename: Tomislav
authors.initials: T
authors.lastname: Ilicic
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Jong Kyoung
authors.initials: JK
authors.lastname: Kim
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.|Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Aleksandra A
authors.initials: AA
authors.lastname: Kolodziejczyk
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.|Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0PT, UK.|National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge, CB2 0PT, UK.
authors.forename: Frederik Otzen
authors.initials: FO
authors.lastname: Bagger
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.|St Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia.
authors.forename: Davis James
authors.initials: DJ
authors.lastname: McCarthy
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.|Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.|University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
authors.forename: John C
authors.initials: JC
authors.lastname: Marioni
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. st9@sanger.ac.uk.|Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. st9@sanger.ac.uk.|Cavendish Laboratory, Dept Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK. st9@sanger.ac.uk.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Teichmann
mesh_terms: D000818:Animals; D001483:Base Sequence / Q000235:genetics*; D001854:Bone Marrow Cells / Q000145:classification; D015496:CD4-Positive T-Lymphocytes / Q000145:classification; D003713:Dendritic Cells / Q000145:classification; D053595:Embryonic Stem Cells / Q000145:classification; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000235:genetics*; D059010:Single-Cell Analysis
chemical_list: D012313:RNA