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Sci Data. 2017 Aug 29;4:170112. doi: 10.1038/sdata.2017.112.

FANTOM5 CAGE profiles of human and mouse samples.

Noguchi S1, Arakawa T1,2, Fukuda S2, Furuno M1,2, Hasegawa A1,2, Hori F1,2, Ishikawa-Kato S1,2, Kaida K2, Kaiho A2, Kanamori-Katayama M2, Kawashima T1,2, Kojima M1,2, Kubosaki A2, Manabe RI1,2, Murata M1,2, Nagao-Sato S1,2, Nakazato K2, Ninomiya N2, Nishiyori-Sueki H1,2, Noma S1,2, Saijyo E2, Saka A2, Sakai M1,2, Simon C2, Suzuki N1,2, Tagami M1,2, Watanabe S1,2, Yoshida S2, Arner P3,4, Axton RA5, Babina M6, Baillie JK7, Barnett TC8,9, Beckhouse AG10, Blumenthal A11, Bodega B12, Bonetti A1,2, Briggs J13, Brombacher F14,15,16, Carlisle AJ7, Clevers HC17,18, Davis CA19, Detmar M20, Dohi T21, Edge ASB22, Edinger M23,24, Ehrlund A3,4, Ekwall K25, Endoh M26, Enomoto H27, Eslami A28, Fagiolini M29, Fairbairn L7, Farach-Carson MC30, Faulkner GJ31, Ferrai C32, Fisher ME7, Forrester LM5, Fujita R33, Furusawa JI26, Geijtenbeek TB34, Gingeras T19, Goldowitz D35, Guhl S6, Guler R14,15,16, Gustincich S36,37, Ha TJ35, Hamaguchi M38, Hara M39, Hasegawa Y1,2, Herlyn M40, Heutink P41, Hitchens KJ8,13, Hume DA7, Ikawa T26, Ishizu Y1,2, Kai C42,43, Kawamoto H26, Kawamura YI21, Kempfle JS22, Kenna TJ44, Kere J25,45, Khachigian LM46,47, Kitamura T48, Klein S20, Klinken SP49, Knox AJ50, Kojima S39, Koseki H26, Koyasu S26, Lee W51, Lennartsson A25, Mackay-Sim A52, Mejhert N3,4, Mizuno Y53, Morikawa H38, Morimoto M27, Moro K26, Morris KJ32, Motohashi H54, Mummery CL55, Nakachi Y53,56, Nakahara F48, Nakamura T42, Nakamura Y57, Nozaki T58, Ogishima S59, Ohkura N38, Ohno H26, Ohshima M60, Okada-Hatakeyama M26,61, Okazaki Y53,56, Orlando V12,62, Ovchinnikov DA13, Passier R55, Patrikakis M46, Pombo A32, Pradhan-Bhatt S63, Qin XY39, Rehli M23,24, Rizzu P41, Roy S2, Sajantila A64, Sakaguchi S38, Sato H42, Satoh H33, Savvi S14,15,16, Saxena A2, Schmidl C23, Schneider C65, Schulze-Tanzil GG66, Schwegmann A14,15,16, Sheng G67, Shin JW1,2, Sugiyama D68, Sugiyama T42, Summers KM7, Takahashi N2, Takai J33, Tanaka H28, Tatsukawa H69, Tomoiu A7, Toyoda H54, van de Wetering M17, van den Berg LM34, Verardo R70, Vijayan D71, Wells CA72, Winteringham LN49, Wolvetang E13, Yamaguchi Y73, Yamamoto M33, Yanagi-Mizuochi C74, Yoneda M42, Yonekura Y27, Zhang PG35, Zucchelli S36, Abugessaisa I1, Arner E1,2, Harshbarger J1,2, Kondo A1,2, Lassmann T1,2,75, Lizio M1,2, Sahin S1,2, Sengstag T2, Severin J1,2, Shimoji H2,76, Suzuki M2, Suzuki H1,2, Kawai J2,77, Kondo N1,2, Itoh M1,2,77, Daub CO1,2,25, Kasukawa T1, Kawaji H1,2,76,77, Carninci P1,2, Forrest ARR1,2,49, Hayashizaki Y2,77.

Author information

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.

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.

PMID:
28850106
PMCID:
PMC5574368
DOI:
10.1038/sdata.2017.112
[Indexed for MEDLINE]
Free PMC Article

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