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Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads.

Autor: De Rop, Florian V., Ismail, Joy N., González-Blas, Carmen Bravo, Hulselmans, Gert J., Flerin, Christopher Campbell, Janssens, Jasper, Theunis, Koen, Christiaens, Valerie M., Wouters, Jasper, Marcassa, Gabriele, de Wit, Joris, Poovathingal, Suresh, Aerts, Stein

Publikováno v: eLife; 4/8/2022, p1-26, 26p

Systematic benchmarking of single-cell ATAC-sequencing protocols.

Autor: 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.

Publikováno v: Nature biotechnology [Nat Biotechnol] 2024 Jun; Vol. 42 (6), pp. 916-926. Date of Electronic Publication: 2023 Aug 03.