دورية أكاديمية
Systematic benchmarking of single-cell ATAC-sequencing protocols.
| العنوان: | Systematic benchmarking of single-cell ATAC-sequencing protocols. |
|---|---|
| المؤلفون: | De Rop FV; VIB Center for Brain and Disease Research, Leuven, Belgium.; Department of Human Genetics, KU Leuven, Leuven, Belgium., Hulselmans G; VIB Center for Brain and Disease Research, Leuven, Belgium.; Department of Human Genetics, KU Leuven, Leuven, Belgium., Flerin C; VIB Center for Brain and Disease Research, Leuven, Belgium.; Department of Human Genetics, KU Leuven, Leuven, Belgium., Soler-Vila P; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain., Rafels A; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain., Christiaens V; VIB Center for Brain and Disease Research, Leuven, Belgium.; Department of Human Genetics, KU Leuven, Leuven, Belgium., González-Blas CB; VIB Center for Brain and Disease Research, Leuven, Belgium.; Department of Human Genetics, KU Leuven, Leuven, Belgium., Marchese D; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain., Caratù G; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain., Poovathingal S; VIB Center for Brain and Disease Research, Leuven, Belgium., Rozenblatt-Rosen O; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Slyper M; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Luo W; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Muus C; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Duarte F; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Shrestha R; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Bagdatli ST; Department of Genetics, Stanford University, Stanford, CA, USA., Corces MR; Gladstone Institute of Neurological Disease, San Francisco, CA, USA., Mamanova L; Wellcome Sanger Institute, Cambridge, UK., Knights A; Wellcome Sanger Institute, Cambridge, UK., Meyer KB; Wellcome Sanger Institute, Cambridge, UK., Mulqueen R; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA., Taherinasab A; Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA.; Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA., Maschmeyer P; Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany., Pezoldt J; Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland., Lambert CLG; Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland., Iglesias M; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain., Najle SR; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain., Dossani ZY; Vitalant Research Institute, San Francisco, CA, USA.; Department of Laboratory Medicine, University of California, San Francisco, CA, USA., Martelotto LG; 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.; University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, Victoria, Australia., Burkett Z; Digital Biology Group, Bio-Rad, Pleasanton, CA, USA., Lebofsky R; Digital Biology Group, Bio-Rad, Pleasanton, CA, USA., Martin-Subero JI; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain.; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain., Pillai S; Vitalant Research Institute, San Francisco, CA, USA.; Department of Laboratory Medicine, University of California, San Francisco, CA, USA., Sebé-Pedrós A; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain.; ICREA, Barcelona, Spain., Deplancke B; Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland., Teichmann SA; Wellcome Sanger Institute, Cambridge, UK.; Department of Physics/Cavendish Laboratory, University of Cambridge, Cambridge, UK., Ludwig LS; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany., Braun TP; Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA.; Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA., Adey AC; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA., Greenleaf WJ; Department of Genetics, Stanford University, Stanford, CA, USA.; Chan Zuckerberg Biohub, San Francisco, CA, USA., Buenrostro JD; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Regev A; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Koch Institute of Integrative Cancer Research, Cambridge, MA, USA.; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA., Aerts S; VIB Center for Brain and Disease Research, Leuven, Belgium. stein.aerts@kuleuven.be.; Department of Human Genetics, KU Leuven, Leuven, Belgium. stein.aerts@kuleuven.be., Heyn H; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. holger.heyn@cnag.crg.eu.; Universitat Pompeu Fabra (UPF), Barcelona, Spain. holger.heyn@cnag.crg.eu. |
| المصدر: | Nature biotechnology [Nat Biotechnol] 2024 Jun; Vol. 42 (6), pp. 916-926. Date of Electronic Publication: 2023 Aug 03. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Nature America Publishing Country of Publication: United States NLM ID: 9604648 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1546-1696 (Electronic) Linking ISSN: 10870156 NLM ISO Abbreviation: Nat Biotechnol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: New York Ny : Nature America Publishing Original Publication: New York, NY : Nature Pub. Co., [1996- |
| مواضيع طبية MeSH: | Single-Cell Analysis*/methods , Benchmarking* , Leukocytes, Mononuclear*, Humans ; Chromatin Immunoprecipitation Sequencing/methods ; Chromatin/genetics ; Transposases/genetics ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods |
| مستخلص: | 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).) |
| References: | Nat Methods. 2019 May;16(5):397-400. (PMID: 30962623) Nat Methods. 2023 Sep;20(9):1355-1367. (PMID: 37443338) Nat Biotechnol. 2021 Apr;39(4):451-461. (PMID: 32788668) Nucleic Acids Res. 2015 Jul 1;43(W1):W57-64. (PMID: 25925574) Genome Biol. 2018 Feb 6;19(1):15. (PMID: 29409532) Nature. 2015 Jul 23;523(7561):486-90. (PMID: 26083756) Nat Methods. 2019 Dec;16(12):1289-1296. (PMID: 31740819) Gigascience. 2021 Feb 16;10(2):. (PMID: 33590861) Nature. 2012 Sep 6;489(7414):57-74. (PMID: 22955616) Nat Biotechnol. 2021 Dec;39(12):1574-1580. (PMID: 34226710) Mol Cell. 2010 May 28;38(4):576-89. (PMID: 20513432) Cell. 2019 Jun 13;177(7):1888-1902.e21. (PMID: 31178118) Nat Rev Methods Primers. 2021;1:. (PMID: 38410680) Elife. 2022 Feb 23;11:. (PMID: 35195064) Nat Biotechnol. 2019 Aug;37(8):916-924. (PMID: 31235917) Cell. 2018 Aug 23;174(5):1309-1324.e18. (PMID: 30078704) BMC Genomics. 2018 Mar 1;19(1):169. (PMID: 29490630) Nat Biotechnol. 2019 Aug;37(8):925-936. (PMID: 31375813) Nat Biotechnol. 2020 Jun;38(6):747-755. (PMID: 32518403) Nat Rev Immunol. 2016 Oct;16(10):626-38. (PMID: 27546235) Science. 2020 Nov 13;370(6518):. (PMID: 33184180) Genome Biol. 2008;9(9):R137. (PMID: 18798982) Cell Syst. 2019 Apr 24;8(4):281-291.e9. (PMID: 30954476) Nat Biotechnol. 2017 Apr 11;35(4):316-319. (PMID: 28398311) Nat Biotechnol. 2020 Jun;38(6):737-746. (PMID: 32341560) Nature. 2015 Oct 1;526(7571):68-74. (PMID: 26432245) Sci Rep. 2019 Jun 27;9(1):9354. (PMID: 31249361) Genome Biol. 2020 May 11;21(1):112. (PMID: 32393363) Cell. 2021 Nov 24;184(24):5985-6001.e19. (PMID: 34774128) Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943) Nat Commun. 2020 Feb 13;11(1):866. (PMID: 32054859) Nucleic Acids Res. 2012 Aug;40(15):e114. (PMID: 22718975) Bioinformatics. 2005 Aug 15;21(16):3439-40. (PMID: 16082012) |
| معلومات مُعتمدة: | R01 DA047237 United States DA NIDA NIH HHS; R00 AG059918 United States AG NIA NIH HHS; U19 AI057266 United States AI NIAID NIH HHS; G0B5619N Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders); RF1 MH128842 United States MH NIMH NIH HHS; UM1 HG009436 United States HG NHGRI NIH HHS; 1S80920N Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders); UM1 HG012076 United States HG NHGRI NIH HHS; RM1 HG007735 United States HG NHGRI NIH HHS; G094121N Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders); R35 GM124704 United States GM NIGMS NIH HHS; UM1 HG009442 United States HG NHGRI NIH HHS; United Kingdom WT_ Wellcome Trust |
| المشرفين على المادة: | 0 (Chromatin) EC 2.7.7.- (Transposases) |
| تواريخ الأحداث: | Date Created: 20230803 Date Completed: 20240616 Latest Revision: 20240620 |
| رمز التحديث: | 20240620 |
| مُعرف محوري في PubMed: | PMC11180611 |
| DOI: | 10.1038/s41587-023-01881-x |
| PMID: | 37537502 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 1546-1696 |
|---|---|
| DOI: | 10.1038/s41587-023-01881-x |