Systematic benchmarking of single-cell ATAC-sequencing protocols

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Cited 11 times in Scopus logo

Cited 14 times in Web of Science logo

Cited 8 times in Europe PMC logo

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H.H. received support for the project PID2020-115439GB-I00 funded by MCIN/AEI/10.13039/501100011033. This publication is also supported as part of a project (BCLLATLAS and ESPACE) that has received funding from the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme (grant agreement numbers 810287 and 874710). This work was supported by a European Research Council Consolidator grant to S.A. (724226_cis-CONTROL), KU Leuven (C14/22/125 to S.A.), Foundation Against Cancer (F/2020/1396 to S.A.), F.W.O. (grants G0I2722N, G0B5619N and G094121N to S.A. and a PhD fellowship to F.D.) and Aligning Science Across Parkinson's (grant number ASAP-000430 to S.A.). K.B.M. and S.A.T. are supported by Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194). Computing was performed at the Vlaams Supercomputer Center and high-throughput sequencing at the Genomics Core Leuven. M.R.C. is supported by the National Institutes on Aging K99/R00AG059918. This work was supported by funding from the Rita Allen Foundation (W.J.G.) and the Human Frontiers Science Program (RGY006S; W.J.G.). W.J.G. is a Chan Zuckerberg Biohub investigator and acknowledges grants 2017-174468 and 2018-182817 from the Chan Zuckerberg Initiative and National Institutes of Health grants RM1-HG007735, UM1-HG009442, UM1-HG009436, R01-HG00990901 and U19-AI057266 (to W.J.G.). W.J.G. acknowledges funding from Emerson Collective. B.D. received financial support by Swiss National Science Foundation 310030_197082 and the EPFL. L.S.L. receives support from an Emmy Noether fellowship by the German Research Foundation (LU 2336/2-1), a National Institutes of Health grant UM1HG012076, a Longevity Impetus grant and a Hector Research Career Development Award by the Hector Fellow Academy. A.C.A. is supported by National Institutes of Health grants RF1-MH128842, R35-GM124704 and R01-DA047237 as well as a Silver Family Foundation Innovator Award.

Analysis of institutional authors

Soler-Vila PAuthorMartin-Subero JiAuthor

August 7, 2023

Publications

Article

Publicated to:Nature Biotechnology. 42 (6): 916-+ - 2024-06-01 42(6), DOI: 10.1038/s41587-023-01881-x

Authors: De Rop, Florian V; Hulselmans, Gert; Flerin, Chris; Soler-Vila, Paula; Rafels, Albert; Christiaens, Valerie; Gonzalez-Blas, Carmen Bravo; Marchese, Domenica; Caratu, Ginevra; Poovathingal, Suresh; Rozenblatt-Rosen, Orit; Slyper, Michael; Luo, Wendy; Muus, Christoph; Duarte, Fabiana; Shrestha, Rojesh; Bagdatli, S Tansu; Corces, M Ryan; Mamanova, Lira; Knights, Andrew; Meyer, Kerstin B; Mulqueen, Ryan; Taherinasab, Akram; Maschmeyer, Patrick; Pezoldt, Jörn; Lambert, Camille Lucie Germaine; Iglesias, Marta; Najle, Sebastian R; Dossani, Zain Y; Martelotto, Luciano G; Burkett, Zach; Lebofsky, Ronald; Martin-Subero, Jose Ignacio; Pillai, Satish; Sebe-Pedros, Arnau; Deplancke, Bart; Teichmann, Sarah A; Ludwig, Leif S; Braun, Theodore P; Greenleaf, William J; Buenrostro, Jason D; Regev, Aviv; Aerts, Stein; Heyn, Holger

Affiliations

Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia. - Author

Barcelona Inst Sci & Technol BIST, Ctr Genom Regulat CRG, CNAG CRG, Barcelona, Spain - Author

Berlin Inst Med Syst Biol BIMSB, Max Delbruck Ctr Mol Med Helmholtz Assoc MDC, Berlin, Germany - Author

Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany. - Author

Bio Rad, Digital Biol Grp, Pleasanton, CA USA - Author

Broad Inst & Harvard, Cambridge, MA USA - Author

Broad Inst & MIT & Harvard, Gene Regulat Observ, Cambridge, MA USA - Author

Broad Inst & MIT & Harvard, Klarman Cell Observ, Cambridge, MA USA - Author

Broad Institute of MIT and Harvard, Cambridge, MA, USA. - Author

Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain. - Author

Chan Zuckerberg Biohub, San Francisco, CA USA - Author

Chan Zuckerberg Biohub, San Francisco, CA, USA. - Author

Charite Univ Med Berlin, Berlin Inst Hlth, Berlin, Germany - Author

CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. - Author

CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. holger.heyn@cnag.crg.eu. - Author

Ctr Invest Biomed Red Canc CIBERONC, Madrid, Spain - Author

Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain. - Author

Department of Genetics, Stanford University, Stanford, CA, USA. - Author

Department of Human Genetics, KU Leuven, Leuven, Belgium. - Author

Department of Human Genetics, KU Leuven, Leuven, Belgium. stein.aerts@kuleuven.be. - Author

Department of Laboratory Medicine, University of California, San Francisco, CA, USA. - Author

Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA. - Author

Department of Physics/Cavendish Laboratory, University of Cambridge, Cambridge, UK. - Author

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. - Author

Digital Biology Group, Bio-Rad, Pleasanton, CA, USA. - Author

Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA. - Author

Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA. - Author

Ecole Polytech Fed Lausanne EPFL, Inst Bioengn, Sch Life Sci, Lab Syst Biol & Genet, Lausanne, Switzerland - Author

Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. - Author

Gladstone Inst Neurol Dis, San Francisco, CA USA - Author

Gladstone Institute of Neurological Disease, San Francisco, CA, USA. - Author

Harvard Univ, Dept Stem Cell & Regenerat Biol, Cambridge, MA USA - Author

Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. - Author

ICREA, Barcelona, Spain - Author

ICREA, Barcelona, Spain. - Author

Inst Catalana Recerca & Estudis Avancats ICREA, Barcelona, Spain - Author

Inst Invest Biomed August Pi i Sunyer IDIBAPS, Barcelona, Spain - Author

Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain. - Author

Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. - Author

Katholieke Univ Leuven, Dept Human Genet, Leuven, Belgium - Author

Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. - Author

Koch Inst Integrat Canc Res, Cambridge, MA USA - Author

Koch Institute of Integrative Cancer Research, Cambridge, MA, USA. - Author

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. - Author

Massachusetts Inst Technol MIT, Howard Hughes Med Inst, Dept Biol, Cambridge, MA USA - Author

Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany. - Author

Oregon Hlth & Sci Univ, Dept Mol & Med Genet, Portland, OR USA - Author

Oregon Hlth & Sci Univ, Knight Canc Inst, Div Hematol & Med Oncol, Portland, OR USA - Author

Oregon Hlth & Sci Univ, Knight Canc Inst, Div Oncol Sci, Portland, OR USA - Author

Stanford Univ, Dept Genet, Stanford, CA USA - Author

Swiss Inst Bioinformat SIB, Lausanne, Switzerland - Author

Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland. - Author

Univ Adelaide, Adelaide Ctr Epigenet, Fac Hlth & Med Sci, Adelaide, SA, Australia - Author

Univ Adelaide, South Australian Immunogen Canc Inst, Fac Hlth & Med Sci, Adelaide, SA, Australia - Author

Univ Barcelona, Dept Fonaments Clin, Fac Med, Barcelona, Spain - Author

Univ Calif San Francisco, Dept Lab Med, San Francisco, CA USA - Author

Univ Cambridge, Dept Phys, Cavendish Lab, Cambridge, England - Author

Univ Melbourne, Victoria Comprehens Canc Ctr, Ctr Canc Res, Melbourne, Vic, Australia - Author

Univ Pompeu Fabra UPF, Barcelona, Spain - Author

Universitat Pompeu Fabra (UPF), Barcelona, Spain. - Author

Universitat Pompeu Fabra (UPF), Barcelona, Spain. holger.heyn@cnag.crg.eu. - Author

University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, Victoria, Australia. - Author

VIB Center for Brain and Disease Research, Leuven, Belgium. - Author

VIB Center for Brain and Disease Research, Leuven, Belgium. stein.aerts@kuleuven.be. - Author

VIB Ctr Brain & Dis Res, Leuven, Belgium - Author

Vitalant Res Inst, San Francisco, CA USA - Author

Vitalant Research Institute, San Francisco, CA, USA. - Author

Wellcome Sanger Inst, Cambridge, England - Author

Wellcome Sanger Institute, Cambridge, UK. - Author

Abstract

Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols.© 2023. The Author(s).

Keywords

Analysis protocolArticleAutoanalysisBenchmarkingCell typesCells by body anatomyCellularsChromatinChromatin immunoprecipitation sequencingControlled studyCytologyData analysisData handlingDna sequencingExtractionGene expressionGeneticsGenotypeHigh throughput sequencingHigh-throughput nucleotide sequencingHumanHuman cellHuman peripheral bloodHumansLeukocytes, mononuclearMononuclear cellPerformancePeripheral blood mononuclear cellPeripheral blood mononuclear cellsPipelinePipelinesProceduresSensitivity and specificitySequence analysis, dnaSequencing methodSex differenceSingle cell analysisSingle cell assaysSingle cellsSingle-cell analysisSmall cytoplasmic rnaTranscriptionTranscription factorTransposaseTransposasesType annotations

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nature Biotechnology due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2024 there are still no calculated indicators, but in 2023, it was in position 2/177, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biotechnology & Applied Microbiology. Notably, the journal is positioned above the 90th percentile.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 14.1, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Aug 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-08-12, the following number of citations:

WoS: 14
Scopus: 11
Europe PMC: 8

Impact and social visibility

Leadership analysis of institutional authors