Pulling out the 1%:whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries

Autor: Nikola Theodossiev, Cristina Valdiosera, Simon Gravel, Diana Dimitrova, Yingrui Li, Krasimir Leshtakov, M. Thomas P. Gilbert, William J. Greenleaf, Martin Sikora, Andrés Moreno-Estrada, Meredith L. Carpenter, Morten E. Allentoft, Sonia Guillén, Hannes Schroeder, Eske Willerslev, Georgi Nekhrizov, Karla Sandoval, Jason D. Buenrostro, Morten Rasmussen, Jun Wang, Davide Pettener, Carlos Bustamante, Donata Luiselli

Publikováno v: Carpenter, M L, Buenrostro, J D, Valdiosera Morales, C, Schroeder, H, Allentoft, M E, Sikora, M, Rasmussen, M, Gravel, S, Guillén, S, Nekhrizov, G, Leshtakov, K, Dimitrova, D, Theodossiev, N, Pettener, D, Luiselli, D, Sandoval, K, Moreno-Estrada, A, Li, Y, Wang, J, Gilbert, T, Willerslev, E, Greenleaf, W J & Bustamante, C D 2013, ' Pulling out the 1% : whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries ', American Journal of Human Genetics, vol. 93, no. 5, pp. 852-864 . https://doi.org/10.1016/j.ajhg.2013.10.002

Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::24f37d845f2cfe96274198bca225d7a7
https://curis.ku.dk/ws/files/184637852/Carpenter_2013_Pulling_out_the_1.pdf

Expansion in situ genome sequencing links nuclear abnormalities to hotspots of aberrant euchromatin repression.

Autor: Labade AS, Chiang ZD, Comenho C, Reginato PL, Payne AC, Earl AS, Shrestha R, Duarte FM, Habibi E, Zhang R, Church GM, Boyden ES, Chen F, Buenrostro JD

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Sep 26. Date of Electronic Publication: 2024 Sep 26.

BACH2 regulates diversification of regulatory and proinflammatory chromatin states in T H 17 cells.

Autor: Thakore PI; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Genentech, South San Francisco, CA, USA., Schnell A; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Huang L; The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.; Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA., Zhao M; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Hou Y; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA., Christian E; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Zaghouani S; The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA., Wang C; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.; Department of Immunology, University of Toronto and Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada., Singh V; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Singaraju A; The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA., Krishnan RK; The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA., Kozoriz D; The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA., Ma S; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA., Sankar V; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Notarbartolo S; Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland.; Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Infectious Diseases Unit, Milan, Italy., 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., Sallusto F; Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland.; Institute of Microbiology, ETH Zurich, Zurich, Switzerland., Patsopoulos NA; Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham & Women's Hospital, Boston, MA, USA.; Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Rozenblatt-Rosen O; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Genentech, South San Francisco, CA, USA., Kuchroo VK; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. vkuchroo@bwh.harvard.edu.; The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. vkuchroo@bwh.harvard.edu., Regev A; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. aviv.regev.sc@gmail.com.; Genentech, South San Francisco, CA, USA. aviv.regev.sc@gmail.com.

Publikováno v: Nature immunology [Nat Immunol] 2024 Aug; Vol. 25 (8), pp. 1395-1410. Date of Electronic Publication: 2024 Jul 15.

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.

Author Correction: Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling.

Autor: Lareau CA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. clareau@broadinstitute.org.; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. clareau@broadinstitute.org.; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA. clareau@broadinstitute.org., Ludwig LS; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. ludwig@broadinstitute.org.; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. ludwig@broadinstitute.org., Muus C; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA., Gohil SH; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Academic Haematology, UCL Cancer Institute, London, UK., Zhao T; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA., Chiang Z; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA., Pelka K; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Verboon JM; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Luo W; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Christian E; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA., Rosebrock D; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Getz G; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Pathology, Harvard Medical School, Boston, MA, USA., Boland GM; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Chen F; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Buenrostro JD; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA., Hacohen N; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Wu CJ; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Aryee MJ; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Pathology, Harvard Medical School, Boston, MA, USA.; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA., Regev A; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. aregev@broadinstitute.org.; Howard Hughes Medical Institute, Chevy Chase, MD, USA. aregev@broadinstitute.org.; Department of Biology and Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. aregev@broadinstitute.org., Sankaran VG; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. sankaran@broadinstitute.org.; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. sankaran@broadinstitute.org.; Harvard Stem Cell Institute, Cambridge, MA, USA. sankaran@broadinstitute.org.

Publikováno v: Nature biotechnology [Nat Biotechnol] 2023 Sep; Vol. 41 (9), pp. 1345.