. 2017 Aug 29:4:170112.

doi: 10.1038/sdata.2017.112.

FANTOM5 CAGE profiles of human and mouse samples

Shuhei Noguchi¹, Takahiro Arakawa^{1

2}, Shiro Fukuda², Masaaki Furuno^{1

2}, Akira Hasegawa^{1

2}, Fumi Hori^{1

2}, Sachi Ishikawa-Kato^{1

2}, Kaoru Kaida², Ai Kaiho², Mutsumi Kanamori-Katayama², Tsugumi Kawashima^{1

2}, Miki Kojima^{1

2}, Atsutaka Kubosaki², Ri-Ichiroh Manabe^{1

2}, Mitsuyoshi Murata^{1

2}, Sayaka Nagao-Sato^{1

2}, Kenichi Nakazato², Noriko Ninomiya², Hiromi Nishiyori-Sueki^{1

2}, Shohei Noma^{1

2}, Eri Saijyo², Akiko Saka², Mizuho Sakai^{1

2}, Christophe Simon², Naoko Suzuki^{1

2}, Michihira Tagami^{1

2}, Shoko Watanabe^{1

2}, Shigehiro Yoshida², Peter Arner^{3

4}, Richard A Axton⁵, Magda Babina⁶, J Kenneth Baillie⁷, Timothy C Barnett^{8

9}, Anthony G Beckhouse¹⁰, Antje Blumenthal¹¹, Beatrice Bodega¹², Alessandro Bonetti^{1

2}, James Briggs¹³, Frank Brombacher^{14

15

16}, Ailsa J Carlisle⁷, Hans C Clevers^{17

18}, Carrie A Davis¹⁹, Michael Detmar²⁰, Taeko Dohi²¹, Albert S B Edge²², Matthias Edinger^{23

24}, Anna Ehrlund^{3

4}, Karl Ekwall²⁵, Mitsuhiro Endoh²⁶, Hideki Enomoto²⁷, Afsaneh Eslami²⁸, Michela Fagiolini²⁹, Lynsey Fairbairn⁷, Mary C Farach-Carson³⁰, Geoffrey J Faulkner³¹, Carmelo Ferrai³², Malcolm E Fisher⁷, Lesley M Forrester⁵, Rie Fujita³³, Jun-Ichi Furusawa²⁶, Teunis B Geijtenbeek³⁴, Thomas Gingeras¹⁹, Daniel Goldowitz³⁵, Sven Guhl⁶, Reto Guler^{14

15

16}, Stefano Gustincich^{36

37}, Thomas J Ha³⁵, Masahide Hamaguchi³⁸, Mitsuko Hara³⁹, Yuki Hasegawa^{1

2}, Meenhard Herlyn⁴⁰, Peter Heutink⁴¹, Kelly J Hitchens^{8

13}, David A Hume⁷, Tomokatsu Ikawa²⁶, Yuri Ishizu^{1

2}, Chieko Kai^{42

43}, Hiroshi Kawamoto²⁶, Yuki I Kawamura²¹, Judith S Kempfle²², Tony J Kenna⁴⁴, Juha Kere^{25

45}, Levon M Khachigian^{46

47}, Toshio Kitamura⁴⁸, Sarah Klein²⁰, S Peter Klinken⁴⁹, Alan J Knox⁵⁰, Soichi Kojima³⁹, Haruhiko Koseki²⁶, Shigeo Koyasu²⁶, Weonju Lee⁵¹, Andreas Lennartsson²⁵, Alan Mackay-Sim⁵², Niklas Mejhert^{3

4}, Yosuke Mizuno⁵³, Hiromasa Morikawa³⁸, Mitsuru Morimoto²⁷, Kazuyo Moro²⁶, Kelly J Morris³², Hozumi Motohashi⁵⁴, Christine L Mummery⁵⁵, Yutaka Nakachi^{53

56}, Fumio Nakahara⁴⁸, Toshiyuki Nakamura⁴², Yukio Nakamura⁵⁷, Tadasuke Nozaki⁵⁸, Soichi Ogishima⁵⁹, Naganari Ohkura³⁸, Hiroshi Ohno²⁶, Mitsuhiro Ohshima⁶⁰, Mariko Okada-Hatakeyama^{26

61}, Yasushi Okazaki^{53

56}, Valerio Orlando^{12

62}, Dmitry A Ovchinnikov¹³, Robert Passier⁵⁵, Margaret Patrikakis⁴⁶, Ana Pombo³², Swati Pradhan-Bhatt⁶³, Xian-Yang Qin³⁹, Michael Rehli^{23

24}, Patrizia Rizzu⁴¹, Sugata Roy², Antti Sajantila⁶⁴, Shimon Sakaguchi³⁸, Hiroki Sato⁴², Hironori Satoh³³, Suzana Savvi^{14

15

16}, Alka Saxena², Christian Schmidl²³, Claudio Schneider⁶⁵, Gundula G Schulze-Tanzil⁶⁶, Anita Schwegmann^{14

15

16}, Guojun Sheng⁶⁷, Jay W Shin^{1

2}, Daisuke Sugiyama⁶⁸, Takaaki Sugiyama⁴², Kim M Summers⁷, Naoko Takahashi², Jun Takai³³, Hiroshi Tanaka²⁸, Hideki Tatsukawa⁶⁹, Andru Tomoiu⁷, Hiroo Toyoda⁵⁴, Marc van de Wetering¹⁷, Linda M van den Berg³⁴, Roberto Verardo⁷⁰, Dipti Vijayan⁷¹, Christine A Wells⁷², Louise N Winteringham⁴⁹, Ernst Wolvetang¹³, Yoko Yamaguchi⁷³, Masayuki Yamamoto³³, Chiyo Yanagi-Mizuochi⁷⁴, Misako Yoneda⁴², Yohei Yonekura²⁷, Peter G Zhang³⁵, Silvia Zucchelli³⁶, Imad Abugessaisa¹, Erik Arner^{1

2}, Jayson Harshbarger^{1

2}, Atsushi Kondo^{1

2}, Timo Lassmann^{1

2

75}, Marina Lizio^{1

2}, Serkan Sahin^{1

2}, Thierry Sengstag², Jessica Severin^{1

2}, Hisashi Shimoji^{2

76}, Masanori Suzuki², Harukazu Suzuki^{1

2}, Jun Kawai^{2

77}, Naoto Kondo^{1

2}, Masayoshi Itoh^{1

2

77}, Carsten O Daub^{1

2

25}, Takeya Kasukawa¹, Hideya Kawaji^{1

2

76

77}, Piero Carninci^{1

2}, Alistair R R Forrest^{1

2

49}, Yoshihide Hayashizaki^{2

77}

Affiliations

¹ Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
² RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan.
³ Department of Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden.
⁴ Karolinska University Hospital, Center for Metabolism and Endocrinology, 141 86, Stockholm, Sweden.
⁵ Scottish Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK.
⁶ Department of Dermatology and Allergy, Charite University Medicine Berlin, Charitéplatz 1, 10117 Berlin, German.
⁷ The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian EH25 9RG, UK.
⁸ Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, QLD 4072, Australia.
⁹ School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
¹⁰ Bio-Rad Laboratories Pty Ltd, Hercules, California 94547, USA.
¹¹ The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102 Australia.
¹² IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143 Rome, Italy.
¹³ Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, St Lucia, QLD 4072, Australia.
¹⁴ Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.
¹⁵ Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.
¹⁶ International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Anzio Road, Observatory 7925, Cape Town, South Africa.
¹⁷ Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
¹⁸ University Medical Centre Utrecht, Postbus 85500, 3508 GA Utrecht, The Netherlands.
¹⁹ Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11797, USA.
²⁰ Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 3, HCI H 303, 8093 Zurich, Switzerland.
²¹ Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute National Center for Global Health and Medicine, Ichikawa, Chiba 272-8516, Japan.
²² Department of Otology and Laryngology, Harvard Medical School, Boston, Massachusetts 02114, USA.
²³ Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93053 Regensburg, Germany.
²⁴ RCI Regensburg Centre for Interventional Immunology, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93053 Regensburg, Germany.
²⁵ Department of Biosciences and Nutrition, Karolinska Institutet, Halsovagen 7-9, SE-141 83 Huddinge, Sweden.
²⁶ RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
²⁷ Laboratory for Neuronal Differentiation and Regeneration, RIKEN Center for Developmental Biology, Chuou-ku, Kobe 650-0047, Japan.
²⁸ Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan.
²⁹ F.M. Kirby Neurobiology Center, Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
³⁰ The University of Texas Health Science Center at Houston, Houston, TX 77251-1892, USA.
³¹ Cancer Biology Program, Mater Medical Research Institute, South Brisbane, Queensland 4101, Australia.
³² Berlin Institute for Medical Systems Biology, Max Delbrueck Center, Robert Roessle Str.10, 13125 Berlin, Germany.
³³ Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan.
³⁴ Experimental Immunology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
³⁵ Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada.
³⁶ Neuroscience, SISSA, Via Bonomea 265, 34136 Trieste, Italy.
³⁷ Department of Neuroscience and Brian Technologies, Italian Istitute of Technology, Via Morego 30, Genova, Italy.
³⁸ Department of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan.
³⁹ RIKEN Center for Life Science Technologies, Wako, Saitama 351-0198, Japan.
⁴⁰ Melanoma Research Center, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.
⁴¹ German Center for Neurodegenerative Diseases (DZNE)-Tübingen, Otfried Müller Straße 23, 72076 Tübingen, Germany.
⁴² Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
⁴³ International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
⁴⁴ Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, QLD 4102, Australia.
⁴⁵ Department of Genetics and Molecular Medicine, King's College London, Guy's St Thomas Street, London, UK.
⁴⁶ Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia.
⁴⁷ Vascular Biology and Translational Research, School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
⁴⁸ Division of Cellular Therapy and Division of Stem Cell Signaling, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
⁴⁹ Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia.
⁵⁰ Respiratory Medicine, University of Nottingham, Hucknall Road, Nottingham NG5 1PB, UK.
⁵¹ Dermatology, School of Medicine Kyungpook National University, Jung-gu, Daegu 41944, Korea.
⁵² Griffith University, Brisbane, Queensland 4111, Australia.
⁵³ Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan.
⁵⁴ Center for Radioisotope Sciences, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan.
⁵⁵ Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
⁵⁶ Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan.
⁵⁷ Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan.
⁵⁸ Department of Clinical Molecular Genetics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.
⁵⁹ Department of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan.
⁶⁰ Department of Biochemistry, Ohu University School of Pharmaceutical Sciences, Koriyama, Fukushima 963-8611 Japan.
⁶¹ Insitute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
⁶² Environmental Epigenetics Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
⁶³ University of Delaware, Newark, DE 19716 USA.
⁶⁴ Hjelt Institute, Department of Forensic Medicine, University of Helsinki, Kytosuontie 11, 003000 Helsinki, Finland.
⁶⁵ Laboratorio Nazionale CIB, Padriciano, 99 34149, Trieste, Italy.
⁶⁶ Department of Orthopedic, Trauma and Reconstructive Surgery, Charite Universitatsmedizin Berlin, Charitéplatz 1, 10117 Berlin, German.
⁶⁷ International Research Center for Medical Sciences (IRCMS), Kumamoto University, Chuo-ku, Kumamoto 860-0811, Japan.
⁶⁸ Department of Clinical Study, Center for Advanced Medical Innovation, Kyushu University, Higashi-Ku, Fukuoka 812-8582, Japan.
⁶⁹ Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
⁷⁰ Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie (LNCIB), Padriciano 99, 34149 Trieste, Italy.
⁷¹ QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
⁷² Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, MDHS, University of Melbourne, Melbourne, VIC 3010, Australia.
⁷³ Department of Biochemistry, Nihon University School of Dentistry, Chiyoda-ku, Tokyo 101-8310, Japan.
⁷⁴ Center for Clinical and Translational Reseach, Kyushu University Hospital, Higashi-Ku, Fukuoka 812-8582, Japan.
⁷⁵ Telethon Kids Institute, the University of Western Australia, Perth, WA, Australia.
⁷⁶ Preventive medicine and applied genomics unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Kanagawa 230-0045, Japan.
⁷⁷ RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.

PMID: 28850106
PMCID: PMC5574368
DOI: 10.1038/sdata.2017.112

FANTOM5 CAGE profiles of human and mouse samples

Shuhei Noguchi et al. Sci Data. 2017.

. 2017 Aug 29:4:170112.

doi: 10.1038/sdata.2017.112.

Authors

Affiliations

¹ Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
² RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan.
³ Department of Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden.
⁴ Karolinska University Hospital, Center for Metabolism and Endocrinology, 141 86, Stockholm, Sweden.
⁵ Scottish Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK.
⁶ Department of Dermatology and Allergy, Charite University Medicine Berlin, Charitéplatz 1, 10117 Berlin, German.
⁷ The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian EH25 9RG, UK.
⁸ Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, QLD 4072, Australia.
⁹ School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
¹⁰ Bio-Rad Laboratories Pty Ltd, Hercules, California 94547, USA.
¹¹ The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102 Australia.
¹² IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143 Rome, Italy.
¹³ Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, St Lucia, QLD 4072, Australia.
¹⁴ Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.
¹⁵ Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.
¹⁶ International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Anzio Road, Observatory 7925, Cape Town, South Africa.
¹⁷ Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
¹⁸ University Medical Centre Utrecht, Postbus 85500, 3508 GA Utrecht, The Netherlands.
¹⁹ Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11797, USA.
²⁰ Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 3, HCI H 303, 8093 Zurich, Switzerland.
²¹ Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute National Center for Global Health and Medicine, Ichikawa, Chiba 272-8516, Japan.
²² Department of Otology and Laryngology, Harvard Medical School, Boston, Massachusetts 02114, USA.
²³ Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93053 Regensburg, Germany.
²⁴ RCI Regensburg Centre for Interventional Immunology, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93053 Regensburg, Germany.
²⁵ Department of Biosciences and Nutrition, Karolinska Institutet, Halsovagen 7-9, SE-141 83 Huddinge, Sweden.
²⁶ RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
²⁷ Laboratory for Neuronal Differentiation and Regeneration, RIKEN Center for Developmental Biology, Chuou-ku, Kobe 650-0047, Japan.
²⁸ Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan.
²⁹ F.M. Kirby Neurobiology Center, Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
³⁰ The University of Texas Health Science Center at Houston, Houston, TX 77251-1892, USA.
³¹ Cancer Biology Program, Mater Medical Research Institute, South Brisbane, Queensland 4101, Australia.
³² Berlin Institute for Medical Systems Biology, Max Delbrueck Center, Robert Roessle Str.10, 13125 Berlin, Germany.
³³ Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan.
³⁴ Experimental Immunology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
³⁵ Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada.
³⁶ Neuroscience, SISSA, Via Bonomea 265, 34136 Trieste, Italy.
³⁷ Department of Neuroscience and Brian Technologies, Italian Istitute of Technology, Via Morego 30, Genova, Italy.
³⁸ Department of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan.
³⁹ RIKEN Center for Life Science Technologies, Wako, Saitama 351-0198, Japan.
⁴⁰ Melanoma Research Center, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.
⁴¹ German Center for Neurodegenerative Diseases (DZNE)-Tübingen, Otfried Müller Straße 23, 72076 Tübingen, Germany.
⁴² Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
⁴³ International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
⁴⁴ Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, QLD 4102, Australia.
⁴⁵ Department of Genetics and Molecular Medicine, King's College London, Guy's St Thomas Street, London, UK.
⁴⁶ Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia.
⁴⁷ Vascular Biology and Translational Research, School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
⁴⁸ Division of Cellular Therapy and Division of Stem Cell Signaling, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
⁴⁹ Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia.
⁵⁰ Respiratory Medicine, University of Nottingham, Hucknall Road, Nottingham NG5 1PB, UK.
⁵¹ Dermatology, School of Medicine Kyungpook National University, Jung-gu, Daegu 41944, Korea.
⁵² Griffith University, Brisbane, Queensland 4111, Australia.
⁵³ Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan.
⁵⁴ Center for Radioisotope Sciences, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan.
⁵⁵ Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
⁵⁶ Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan.
⁵⁷ Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan.
⁵⁸ Department of Clinical Molecular Genetics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.
⁵⁹ Department of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan.
⁶⁰ Department of Biochemistry, Ohu University School of Pharmaceutical Sciences, Koriyama, Fukushima 963-8611 Japan.
⁶¹ Insitute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
⁶² Environmental Epigenetics Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
⁶³ University of Delaware, Newark, DE 19716 USA.
⁶⁴ Hjelt Institute, Department of Forensic Medicine, University of Helsinki, Kytosuontie 11, 003000 Helsinki, Finland.
⁶⁵ Laboratorio Nazionale CIB, Padriciano, 99 34149, Trieste, Italy.
⁶⁶ Department of Orthopedic, Trauma and Reconstructive Surgery, Charite Universitatsmedizin Berlin, Charitéplatz 1, 10117 Berlin, German.
⁶⁷ International Research Center for Medical Sciences (IRCMS), Kumamoto University, Chuo-ku, Kumamoto 860-0811, Japan.
⁶⁸ Department of Clinical Study, Center for Advanced Medical Innovation, Kyushu University, Higashi-Ku, Fukuoka 812-8582, Japan.
⁶⁹ Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
⁷⁰ Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie (LNCIB), Padriciano 99, 34149 Trieste, Italy.
⁷¹ QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
⁷² Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, MDHS, University of Melbourne, Melbourne, VIC 3010, Australia.
⁷³ Department of Biochemistry, Nihon University School of Dentistry, Chiyoda-ku, Tokyo 101-8310, Japan.
⁷⁴ Center for Clinical and Translational Reseach, Kyushu University Hospital, Higashi-Ku, Fukuoka 812-8582, Japan.
⁷⁵ Telethon Kids Institute, the University of Western Australia, Perth, WA, Australia.
⁷⁶ Preventive medicine and applied genomics unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Kanagawa 230-0045, Japan.
⁷⁷ RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.

PMID: 28850106
PMCID: PMC5574368
DOI: 10.1038/sdata.2017.112

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.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing financial interests.

Figures

**Figure 1. Data processing scheme.**
Data processing scheme from sample preparation to CAGE peak expression and annotation. Sky blue and beige color indicate locations storing the data, the FANTOM5 data archive (Data Citation 1, Data Citations 10) and in DDBJ Sequence Read Archive (Data Citations 2–9) respectively.

**Figure 2. RNA and mapping quality control.**
Distribution of RIN score (a), A260/A230 (b), A260/A280 (c), mapped reads (d), and promoter rate (e) for samples used for FANTOM5 expression analysis.

**Figure 3. Hierarchical clustering of primary cells.**
Hierarchical clustering of primary cell samples of mouse based on logarithm of expression (TPM). Color shows anatomical categories of samples.

See this image and copyright information in PMC

Dataset use reported in

doi: 10.1038/nature13182
doi: 10.1126/science.1259418

References

Data Citations

1. Noguchi S. 2017. figshare. https://doi.org/10.6084/m9.figshare.c.3728767 - DOI
1. 2013. DDBJ Sequence Read Archive. DRA000991
1. 2013. DDBJ Sequence Read Archive. DRA001026
1. 2013. DDBJ Sequence Read Archive. DRA001027
1. 2013. DDBJ Sequence Read Archive. DRA001028

References

1. de Hoon M., Shin J. W. & Carninci P. Paradigm shifts in genomics through the FANTOM projects. Mamm Genome 26, 391–402 (2015). - PMC - PubMed
1. The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. Functional annotation of a full-length mouse cDNA collection. Nature 409, 685–690 (2001). - PubMed
1. The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I & II Team. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563–573 (2002). - PubMed
1. RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium. Antisense transcription in the mammalian transcriptome. Science 309, 1564–1566 (2005). - PubMed
1. The FANTOM Consortium and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group). The Transcriptional Landscape of the Mammalian Genome. Science 309, 1559–1563 (2006). - PubMed

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FANTOM5 CAGE profiles of human and mouse samples

Affiliations

FANTOM5 CAGE profiles of human and mouse samples

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

Dataset use reported in

References

Data Citations

References

Publication types

MeSH terms

Associated data

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Miscellaneous