FANTOM5 CAGE profiles of human and mouse samples
Shuhei Noguchi, Takahiro Arakawa(RIKEN Center for Integrative Medical Sciences), Shiro Fukuda(RIKEN Center for Integrative Medical Sciences), Masaaki Furuno(RIKEN Center for Integrative Medical Sciences), Akira Hasegawa(RIKEN Center for Integrative Medical Sciences), Fumi Hori(RIKEN Center for Integrative Medical Sciences), Sachi Ishikawa-Kato(RIKEN Center for Integrative Medical Sciences), Kaoru Kaida(RIKEN Center for Integrative Medical Sciences), Ai Kaiho(RIKEN Center for Integrative Medical Sciences), Mutsumi Kanamori-Katayama(RIKEN Center for Integrative Medical Sciences), Tsugumi Kawashima(RIKEN Center for Integrative Medical Sciences), Miki Kojima(RIKEN Center for Integrative Medical Sciences), Atsutaka Kubosaki(RIKEN Center for Integrative Medical Sciences), Ri-ichiroh Manabe(RIKEN Center for Integrative Medical Sciences), Mitsuyoshi Murata(RIKEN Center for Integrative Medical Sciences), Sayaka Nagao-Sato(RIKEN Center for Integrative Medical Sciences), Kenichi Nakazato(RIKEN Center for Integrative Medical Sciences), Noriko Ninomiya(RIKEN Center for Integrative Medical Sciences), Hiromi Nishiyori-Sueki(RIKEN Center for Integrative Medical Sciences), Shohei Noma(RIKEN Center for Integrative Medical Sciences), Eri Saijyo(RIKEN Center for Integrative Medical Sciences), Akiko Saka(RIKEN Center for Integrative Medical Sciences), Mizuho Sakai(RIKEN Center for Integrative Medical Sciences), Christophe Simon(RIKEN Center for Integrative Medical Sciences), Naoko Suzuki(RIKEN Center for Integrative Medical Sciences), Michihira Tagami(RIKEN Center for Integrative Medical Sciences), Shoko Watanabe(RIKEN Center for Integrative Medical Sciences), Shigehiro Yoshida(RIKEN Center for Integrative Medical Sciences), Peter Arner(Karolinska University Hospital), Richard A Axton(MRC Centre for Regenerative Medicine), Magda Babina(Charité - Universitätsmedizin Berlin), J. Kenneth Baillie(Roslin Institute), Timothy C. Barnett(The University of Queensland), Anthony G Beckhouse(Bio-Rad (United States)), Antje Blumenthal(Translational Research Institute), Beatrice Bodega(Fondazione Santa Lucia), Alessandro Bonetti(RIKEN Center for Integrative Medical Sciences), James Briggs(The University of Queensland), Frank Brombacher(South African Medical Research Council), Ailsa J Carlisle(Roslin Institute), Hans Clevers(Royal Netherlands Academy of Arts and Sciences), Carrie Davis(Cold Spring Harbor Laboratory), Michael Detmar(ETH Zurich), Taeko Dohi(National Center for Global Health and Medicine), Albert S.B. Edge(Harvard University), Matthias Edinger(University Hospital Regensburg), Anna Ehrlund(Karolinska University Hospital), Karl Ekwall(Karolinska Institutet), Mitsuhiro Endoh(RIKEN Center for Integrative Medical Sciences), Hideki Enomoto(Foundation for Biomedical Research and Innovation), Afsaneh Eslami(Tokyo Medical and Dental University), Michela Fagiolini(Boston Children's Hospital), Lynsey Fairbairn(Roslin Institute), Mary C. Farach‐Carson(The University of Texas Health Science Center at Houston), Geoffrey J. Faulkner(Mater Research), Carmelo Ferrai(Max Delbrück Center), Malcolm E Fisher(Roslin Institute), Lesley M. Forrester(MRC Centre for Regenerative Medicine), Rie Fujita(Tohoku University), Jun-ichi Furusawa(RIKEN Center for Integrative Medical Sciences), Teunis B. H. Geijtenbeek(Amsterdam UMC Location University of Amsterdam), T Gingeras(Cold Spring Harbor Laboratory), Dan Goldowitz(University of British Columbia), Sven Guhl(Charité - Universitätsmedizin Berlin), Reto Guler(South African Medical Research Council), Stefano Gustincich(Scuola Internazionale Superiore di Studi Avanzati), Thomas J Ha(University of British Columbia), Masahide Hamaguchi(Osaka International University), Mitsuko Hara(RIKEN), Yuki Hasegawa(RIKEN Center for Integrative Medical Sciences), Meenhard Herlyn(The Wistar Institute), Peter Heutink(German Center for Neurodegenerative Diseases), Kelly J Hitchens(The University of Queensland), David Hume(Roslin Institute), Tomokatsu Ikawa(RIKEN Center for Integrative Medical Sciences), Yuri Ishizu(RIKEN Center for Integrative Medical Sciences), Chieko Kai(National Institute of Infectious Diseases), Hiroshi Kawamoto(RIKEN Center for Integrative Medical Sciences), Yuki I. Kawamura(National Center for Global Health and Medicine), Judith S. Kempfle(Harvard University), Tony Kenna(Translational Research Institute), Juha Kere(St Thomas' Hospital), Levon M. Khachigian(UNSW Sydney), Toshio Kitamura(Tokyo University of Science), Sarah Klein(ETH Zurich), S. Peter Klinken(Harry Perkins Institute of Medical Research), Alan J. Knox(University of Nottingham), Soichi Kojima(RIKEN), Haruhiko Koseki(RIKEN Center for Integrative Medical Sciences), Shigeo Koyasu(RIKEN Center for Integrative Medical Sciences), Weon-Ju Lee(Kyungpook National University Hospital), Andreas Lennartsson(Karolinska Institutet), Alan Mackay‐Sim(Griffith University), Niklas Mejhert(Karolinska University Hospital), Yosuke Mizuno(Saitama Medical University), Hiromasa Morikawa(Osaka International University), Mitsuru Morimoto(Foundation for Biomedical Research and Innovation), Kazuyo Moro(RIKEN Center for Integrative Medical Sciences), Kelly J Morris(Max Delbrück Center), Hozumi Motohashi(Tohoku University), Christine L. Mummery(Leiden University Medical Center), Yutaka Nakachi(Saitama Medical University), Fumio Nakahara(Tokyo University of Science), Toshiyuki Nakamura(The University of Tokyo), Yukio Nakamura(RIKEN BioResource Research Center), Tadasuke Nozaki(Tokyo University of Pharmacy and Life Sciences), Soichi Ogishima(Tohoku University), Naganari Ohkura(Osaka International University), Hiroshi Ohno(RIKEN Center for Integrative Medical Sciences), Mitsuhiro Ohshima(Ohu University), Mariko Okada(RIKEN Center for Integrative Medical Sciences), Yasushi Okazaki(Saitama Medical University), Valerio Orlando(Fondazione Santa Lucia), Dmitry A. Ovchinnikov(The University of Queensland), Robert Passier(Leiden University Medical Center), Margaret Patrikakis(UNSW Sydney), Ana Pombo(Max Delbrück Center), Swati Pradhan-Bhatt(University of Delaware), Xian‐Yang Qin(RIKEN), Michael Rehli(University Hospital Regensburg), Patrizia Rizzu(German Center for Neurodegenerative Diseases), Sugata Roy(RIKEN Center for Integrative Medical Sciences), Antti Sajantila(University of Helsinki), Shimon Sakaguchi(Osaka International University), Hiroki Sato(The University of Tokyo), Hironori Satoh(Tohoku University), Suzana Savvi(South African Medical Research Council), Alka Saxena(RIKEN Center for Integrative Medical Sciences), Christian Schmidl(University Hospital Regensburg), Claudio Schneider(Consorzio Interuniversitario per le Biotecnologie), Gundula Schulze‐Tanzil(Charité - Universitätsmedizin Berlin), Anita Schwegmann(South African Medical Research Council), Guojun Sheng(Kumamoto University), Jay W. Shin(RIKEN Center for Integrative Medical Sciences), Daisuke Sugiyama(Kyushu University), Takaaki Sugiyama(The University of Tokyo), Kim Summers(Roslin Institute), Naoko Takahashi(RIKEN Center for Integrative Medical Sciences), Jun Takai(Tohoku University), Hiroshi Tanaka(Tokyo Medical and Dental University), Hideki Tatsukawa(Nagoya University), Andru Tomoiu(Roslin Institute), Hiroo Toyoda(Tohoku University), Marc van de Wetering(Royal Netherlands Academy of Arts and Sciences), Linda Berg(Amsterdam UMC Location University of Amsterdam), Roberto Verardo(Consorzio Interuniversitario per le Biotecnologie), Dipti Vijayan(QIMR Berghofer Medical Research Institute), Christine A. Wells(The University of Melbourne), Louise N Winteringham(Harry Perkins Institute of Medical Research), Ernst J. Wolvetang(The University of Queensland), Yoko Yamaguchi(Nihon University), Masayuki Yamamoto(Tohoku University), Chiyo Yanagi-Mizuochi(Kyushu University Hospital), Misako Yoneda(The University of Tokyo), Yohei Yonekura(Foundation for Biomedical Research and Innovation), Peter Zhang(University of British Columbia), S. Zucchelli(Scuola Internazionale Superiore di Studi Avanzati), Imad Abugessaisa, Erik Arner(RIKEN Center for Integrative Medical Sciences), Jayson Harshbarger(RIKEN Center for Integrative Medical Sciences), Atsushi Kondo(RIKEN Center for Integrative Medical Sciences), Timo Lassmann(The Kids Research Institute Australia), Marina Lizio(RIKEN Center for Integrative Medical Sciences), Serkan Sahin(RIKEN Center for Integrative Medical Sciences), Thierry Sengstag(RIKEN Center for Integrative Medical Sciences), Jessica Severin(RIKEN Center for Integrative Medical Sciences), Hisashi Shimoji(RIKEN Center for Integrative Medical Sciences), Masanori Suzuki(RIKEN Center for Integrative Medical Sciences), Harukazu Suzuki(RIKEN Center for Integrative Medical Sciences), Jun Kawai(RIKEN), Naoto Kondo(RIKEN Center for Integrative Medical Sciences), Masayoshi Itoh(RIKEN), Carsten O. Daub(Karolinska Institutet), Takeya Kasukawa, Hideya Kawaji(RIKEN), Piero Carninci(RIKEN Center for Integrative Medical Sciences), Alistair R. R. Forrest(Harry Perkins Institute of Medical Research), Yoshihide Hayashizaki(RIKEN)
Cited by 361Open Access
Abstract
In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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