title: Comparative Analysis of Single-Cell RNA Sequencing Methods.
abstract: Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data from 583 mouse embryonic stem cells to evaluate six prominent scRNA-seq methods: CEL-seq2, Drop-seq, MARS-seq, SCRB-seq, Smart-seq, and Smart-seq2. While Smart-seq2 detected the most genes per cell and across cells, CEL-seq2, Drop-seq, MARS-seq, and SCRB-seq quantified mRNA levels with less amplification noise due to the use of unique molecular identifiers (UMIs). Power simulations at different sequencing depths showed that Drop-seq is more cost-efficient for transcriptome quantification of large numbers of cells, while MARS-seq, SCRB-seq, and Smart-seq2 are more efficient when analyzing fewer cells. Our quantitative comparison offers the basis for an informed choice among six prominent scRNA-seq methods, and it provides a framework for benchmarking further improvements of scRNA-seq protocols.
authors.affiliation: Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Ziegenhain
authors.affiliation: Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany.
authors.forename: Beate
authors.initials: B
authors.lastname: Vieth
authors.affiliation: Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany.
authors.forename: Swati
authors.initials: S
authors.lastname: Parekh
authors.affiliation: Ludwig Institute for Cancer Research, Box 240, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
authors.forename: Björn
authors.initials: B
authors.lastname: Reinius
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Amy
authors.initials: A
authors.lastname: Guillaumet-Adkins
authors.affiliation: Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany.
authors.forename: Martha
authors.initials: M
authors.lastname: Smets
authors.affiliation: Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany.
authors.forename: Heinrich
authors.initials: H
authors.lastname: Leonhardt
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Holger
authors.initials: H
authors.lastname: Heyn
authors.affiliation: Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany.
authors.forename: Ines
authors.initials: I
authors.lastname: Hellmann
authors.affiliation: Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany. Electronic address: enard@bio.lmu.de.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Enard
mesh_terms: D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D003198:Computer Simulation; D003362:Cost-Benefit Analysis; D053595:Embryonic Stem Cells / Q000737:chemistry*; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics; D051379:Mice; D018803:Models, Economic; D012313:RNA / Q000235:genetics* / Q000302:isolation & purification; D017423:Sequence Analysis, RNA / Q000191:economics / Q000379:methods*; D059010:Single-Cell Analysis / Q000191:economics / Q000379:methods*
chemical_list: D012313:RNA
keywords: cost-effectiveness; method comparison; power analysis; simulation; single-cell RNA-seq; transcriptomics