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Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

View ORCID ProfileElisabetta Mereu, View ORCID ProfileAtefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J. MacCarthy, Adrian Alvarez, Eduard Batlle, Sagar, Dominic Grün, Julia K. Lau, Stéphane C. Boutet, Chad Sanada, Aik Ooi, Robert C. Jones, Kelly Kaihara, Chris Brampton, Yasha Talaga, Yohei Sasagawa, Kaori Tanaka, Tetsutaro Hayashi, Itoshi Nikaido, Cornelius Fischer, Sascha Sauer, Timo Trefzer, Christian Conrad, Xian Adiconis, Lan T. Nguyen, Aviv Regev, View ORCID ProfileJoshua Z. Levin, Swati Parekh, Aleksandar Janjic, Lucas E. Wange, Johannes W. Bagnoli, Wolfgang Enard, View ORCID ProfileMarta Gut, Rickard Sandberg, Ivo Gut, Oliver Stegle, View ORCID ProfileHolger Heyn
doi: https://doi.org/10.1101/630087
Elisabetta Mereu
1CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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  • ORCID record for Elisabetta Mereu
Atefeh Lafzi
1CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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Catia Moutinho
1CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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Christoph Ziegenhain
2Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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Davis J. MacCarthy
3European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
4European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
5St Vincent’s Institute of Medical Research, Fitzroy, Victoria 3065, Australia
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Adrian Alvarez
6Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona, Spain
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Eduard Batlle
6Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona, Spain
7ICREA, Barcelona, Spain
8Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
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Sagar
9Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
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Dominic Grün
9Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
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Julia K. Lau
1010x Genomics, Pleasanton, CA, USA
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Stéphane C. Boutet
1010x Genomics, Pleasanton, CA, USA
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Chad Sanada
11Fluidigm Corporation, South San Francisco, USA
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Aik Ooi
11Fluidigm Corporation, South San Francisco, USA
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Robert C. Jones
12Department of Bioengineering, Stanford University, Stanford, CA, USA
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Kelly Kaihara
13Bio-Rad, Hercules, CA, USA
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Chris Brampton
13Bio-Rad, Hercules, CA, USA
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Yasha Talaga
13Bio-Rad, Hercules, CA, USA
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Yohei Sasagawa
14Laboratory for Bioinformatics Research RIKEN Center for Biosystems, Dynamics Research, Saitama, Japan
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Kaori Tanaka
14Laboratory for Bioinformatics Research RIKEN Center for Biosystems, Dynamics Research, Saitama, Japan
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Tetsutaro Hayashi
14Laboratory for Bioinformatics Research RIKEN Center for Biosystems, Dynamics Research, Saitama, Japan
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Itoshi Nikaido
14Laboratory for Bioinformatics Research RIKEN Center for Biosystems, Dynamics Research, Saitama, Japan
15Bioinformatics Course, Master’s/Doctoral Program in Life Science, Innovation (T-LSI), School of Integrative and Global Majors (SIGMA), University of Tsukuba, Wako, Saitama, Japan
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Cornelius Fischer
16Max Delbrück Center for Molecular Medicine (BIMSB/BIH), Berlin, Germany
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Sascha Sauer
16Max Delbrück Center for Molecular Medicine (BIMSB/BIH), Berlin, Germany
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Timo Trefzer
17Digital Health Center, Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Berlin, Germany
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Christian Conrad
17Digital Health Center, Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Berlin, Germany
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Xian Adiconis
18Klarman Cell Observatory, Broad Institute of MIT & Harvard, Cambridge, MA, USA
19Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, USA
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Lan T. Nguyen
18Klarman Cell Observatory, Broad Institute of MIT & Harvard, Cambridge, MA, USA
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Aviv Regev
18Klarman Cell Observatory, Broad Institute of MIT & Harvard, Cambridge, MA, USA
20Koch Institute of Integrative Cancer Research, Cambridge, MA, USA
21Howard Hughes Medical Institute, Dept. of Biology, MIT, Cambridge, MA, USA
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Joshua Z. Levin
18Klarman Cell Observatory, Broad Institute of MIT & Harvard, Cambridge, MA, USA
19Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, USA
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Swati Parekh
22Max-Planck-Institute for Biology of Ageing, Cologne, Germany
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Aleksandar Janjic
23Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Martinsried, Germany
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Lucas E. Wange
23Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Martinsried, Germany
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Johannes W. Bagnoli
23Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Martinsried, Germany
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Wolfgang Enard
23Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Martinsried, Germany
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Marta Gut
1CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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Rickard Sandberg
2Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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Ivo Gut
1CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
24Universitat Pompeu Fabra (UPF), Barcelona, Spain
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Oliver Stegle
3European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
4European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
25Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Holger Heyn
1CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
24Universitat Pompeu Fabra (UPF), Barcelona, Spain
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  • For correspondence: holger.heyn@cnag.crg.eu
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Abstract

Single-cell RNA sequencing (scRNA-seq) is the leading technique for charting the molecular properties of individual cells. The latest methods are scalable to thousands of cells, enabling in-depth characterization of sample composition without prior knowledge. However, there are important differences between scRNA-seq techniques, and it remains unclear which are the most suitable protocols for drawing cell atlases of tissues, organs and organisms. We have generated benchmark datasets to systematically evaluate techniques in terms of their power to comprehensively describe cell types and states. We performed a multi-center study comparing 13 commonly used single-cell and single-nucleus RNA-seq protocols using a highly heterogeneous reference sample resource. Comparative and integrative analysis at cell type and state level revealed marked differences in protocol performance, highlighting a series of key features for cell atlas projects. These should be considered when defining guidelines and standards for international consortia, such as the Human Cell Atlas project.

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Posted May 13, 2019.
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Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects
Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J. MacCarthy, Adrian Alvarez, Eduard Batlle, Sagar, Dominic Grün, Julia K. Lau, Stéphane C. Boutet, Chad Sanada, Aik Ooi, Robert C. Jones, Kelly Kaihara, Chris Brampton, Yasha Talaga, Yohei Sasagawa, Kaori Tanaka, Tetsutaro Hayashi, Itoshi Nikaido, Cornelius Fischer, Sascha Sauer, Timo Trefzer, Christian Conrad, Xian Adiconis, Lan T. Nguyen, Aviv Regev, Joshua Z. Levin, Swati Parekh, Aleksandar Janjic, Lucas E. Wange, Johannes W. Bagnoli, Wolfgang Enard, Marta Gut, Rickard Sandberg, Ivo Gut, Oliver Stegle, Holger Heyn
bioRxiv 630087; doi: https://doi.org/10.1101/630087
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Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects
Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J. MacCarthy, Adrian Alvarez, Eduard Batlle, Sagar, Dominic Grün, Julia K. Lau, Stéphane C. Boutet, Chad Sanada, Aik Ooi, Robert C. Jones, Kelly Kaihara, Chris Brampton, Yasha Talaga, Yohei Sasagawa, Kaori Tanaka, Tetsutaro Hayashi, Itoshi Nikaido, Cornelius Fischer, Sascha Sauer, Timo Trefzer, Christian Conrad, Xian Adiconis, Lan T. Nguyen, Aviv Regev, Joshua Z. Levin, Swati Parekh, Aleksandar Janjic, Lucas E. Wange, Johannes W. Bagnoli, Wolfgang Enard, Marta Gut, Rickard Sandberg, Ivo Gut, Oliver Stegle, Holger Heyn
bioRxiv 630087; doi: https://doi.org/10.1101/630087

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