Data Descriptor: FANTOM5 CAGE profiles of human and mouse samples

Shuhei Noguchi; Takahiro Arakawa; Shiro Fukuda; Masaaki Furuno; Akira Hasegawa; Fumi Hori; Sachi Ishikawa-Kato; Kaoru Kaida; Ai Kaiho; Mutsumi Kanamori-Katayama; Tsugumi Kawashima; Miki Kojima; Atsutaka Kubosaki; Ri-ichiroh Manabe; Mitsuyoshi Murata; Sayaka Nagao-Sato; Kenichi Nakazato; Noriko Ninomiya; Hiromi Nishiyori-Sueki; Shohei Noma; Eri Saijyo; Akiko Saka; Mizuho Sakai; Christophe Simon; Naoko Suzuki; Michihira Tagami; Shoko Watanabe; Shigehiro Yoshida; Peter Arner; Richard A. Axton; Magda Babina; J. Kenneth Baillie; Timothy C. Barnett; Anthony G. Beckhouse; Antje Blumenthal; Beatrice Bodega; Alessandro Bonetti; James Briggs; Frank Brombacher; Ailsa J. Carlisle; Hans C. Clevers; Carrie A. Davis; Michael Detmar; Taeko Dohi; Albert S. B. Edge; Matthias Edinger; Anna Ehrlund; Karl Ekwall; Mitsuhiro Endoh; Hideki Enomoto; Afsaneh Eslami; Michela Fagiolini; Lynsey Fairbairn; Mary C. Farach-Carson; Geoffrey J. Faulkner; Carmelo Ferrai; Malcolm E. Fisher; Lesley M. Forrester; Rie Fujita; Jun-ichi Furusawa; Teunis B. Geijtenbeek; Thomas Gingeras; Daniel Goldowitz; Sven Guhl; Reto Guler; Stefano Gustincich; Thomas J. Ha; Masahide Hamaguchi; Mitsuko Hara; Yuki Hasegawa; Meenhard Herlyn; Peter Heutink; Kelly J. Hitchens; David A. Hume; Tomokatsu Ikawa; Yuri Ishizu; Chieko Kai; Hiroshi Kawamoto; Yuki I. Kawamura; Judith S. Kempfle; Tony J. Kenna; Juha Kere; Levon M. Khachigian; Toshio Kitamura; Sarah Klein; S. Peter Klinken; Alan J. Knox; Soichi Kojima; Haruhiko Koseki; Shigeo Koyasu; Weonju Lee; Andreas Lennartsson; Alan Mackay-sim; Niklas Mejhert; Yosuke Mizuno; Hiromasa Morikawa; Mitsuru Morimoto; Kazuyo Moro; Kelly J. Morris; Hozumi Motohashi; Christine L. Mummery; Yutaka Nakachi; Fumio Nakahara; Toshiyuki Nakamura; Yukio Nakamura; Tadasuke Nozaki; Soichi Ogishima; Naganari Ohkura; Hiroshi Ohno; Mitsuhiro Ohshima; Mariko Okada-Hatakeyama; Yasushi Okazaki; Valerio Orlando; Dmitry A. Ovchinnikov; Robert Passier; Margaret Patrikakis; Ana Pombo; Swati Pradhan-Bhatt; Xian-Yang Qin; Michael Rehli; Patrizia Rizzu; Sugata Roy; Antti Sajantila; Shimon Sakaguchi; Hiroki Sato; Hironori Satoh; Suzana Savvi; Alka Saxena; Christian Schmidl; Claudio Schneider; Gundula G. Schulze-Tanzil; Anita Schwegmann; Guojun Sheng; Jay W. Shin; Daisuke Sugiyama; Takaaki Sugiyama; Kim M. Summers; Naoko Takahashi; Jun Takai; Hiroshi Tanaka; Hideki Tatsukawa; Andru Tomoiu; Hiroo Toyoda; Marc van de Wetering; Linda M. van den Berg; Roberto Verardo; Dipti Vijayan; Christine A. Wells; Louise N. Winteringham; Ernst Wolvetang; Yoko Yamaguchi; Masayuki Yamamoto; Chiyo Yanagi-Mizuochi; Misako Yoneda; Yohei Yonekura; Peter G. Zhang; Silvia Zucchelli; Imad Abugessaisa; Erik Arner; Jayson Harshbarger; Atsushi Kondo; Timo Lassmann; Marina Lizio; Serkan Sahin; Thierry Sengstag; Jessica Severin; Hisashi Shimoji; Masanori Suzuki; Harukazu Suzuki; Jun Kawai; Naoto Kondo; Masayoshi Itoh; Carsten O. Daub; Takeya Kasukawa; Hideya Kawaji; Piero Carninci; Alistair R. R. Forrest; Yoshihide Hayashizaki

doi:10.1038/sdata.2017.112

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Data Descriptor: FANTOM5 CAGE profiles of human and mouse samples

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Data Descriptor: FANTOM5 CAGE profiles of human and mouse samples

Shuhei Noguchi, Takahiro Arakawa, Shiro Fukuda, Masaaki Furuno, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Kaoru Kaida, Ai Kaiho, Mutsumi Kanamori-Katayama, …

Scientific data, Vol.4

29/08/2017

DOI: https://doi.org/10.1038/sdata.2017.112

PMID: 28850106

Abstract

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

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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Title: Data Descriptor: FANTOM5 CAGE profiles of human and mouse samples
Creators - without role: Shuhei Noguchi - RIKEN
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
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 Institutet
Richard A. Axton - MRC Centre for Regenerative Medicine
Magda Babina - Charité - Universitätsmedizin Berlin
J. Kenneth Baillie - Roslin Institute
Timothy C. Barnett - University of Queensland
Anthony G. Beckhouse - Bio-Rad
Antje Blumenthal - University of Queensland
Beatrice Bodega - Fondazione Santa Lucia
Alessandro Bonetti - RIKEN Center for Integrative Medical Sciences
James Briggs - University of Queensland
Frank Brombacher - International Centre for Genetic Engineering and Biotechnology
Ailsa J. Carlisle - Roslin Institute
Hans C. Clevers - Royal Netherlands Academy of Arts and Sciences
Carrie A. Davis - Cold Spring Harbor Laboratory
Michael Detmar - ETH Zurich
Taeko Dohi - National Center for Global Health and Medicine
Albert S. B. Edge - Supreme Council Of Health
Matthias Edinger - University Hospital Regensburg
Anna Ehrlund - Karolinska Institutet
Karl Ekwall - Karolinska Institutet
Mitsuhiro Endoh - RIKEN Center for Integrative Medical Sciences
Hideki Enomoto - RIKEN Center for Brain Science
Afsaneh Eslami - Tokyo Medical and Dental University
Michela Fagiolini - Harvard University
Lynsey Fairbairn - University of Edinburgh
Mary C. Farach-Carson - The University of Texas Health Science Center at Houston
Geoffrey J. Faulkner - Mater Research
Carmelo Ferrai - Max Delbrück Center for Molecular Medicine
Malcolm E. Fisher - University of Edinburgh
Lesley M. Forrester - MRC Centre for Regenerative Medicine
Rie Fujita - Tohoku University
Jun-ichi Furusawa - RIKEN Center for Integrative Medical Sciences
Teunis B. Geijtenbeek - University of Amsterdam
Thomas Gingeras - Cold Spring Harbor Laboratory
Daniel Goldowitz - University of British Columbia
Sven Guhl - Charité - Universitätsmedizin Berlin
Reto Guler - International Centre for Genetic Engineering and Biotechnology
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 - University of Queensland
David A. Hume - Roslin Institute
Tomokatsu Ikawa - RIKEN Center for Integrative Medical Sciences
Yuri Ishizu - RIKEN Center for Integrative Medical Sciences
Chieko Kai - The University of Tokyo
Hiroshi Kawamoto - RIKEN Center for Integrative Medical Sciences
Yuki I. Kawamura - National Center for Global Health and Medicine
Judith S. Kempfle - Harvard University
Tony J. Kenna - Princess Alexandra Hospital
Juha Kere - King's College London
Levon M. Khachigian - UNSW Sydney
Toshio Kitamura - The University of Tokyo
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
Weonju Lee - Supreme Council Of Health
Andreas Lennartsson - Karolinska Institutet
Alan Mackay-sim - Griffith University
Niklas Mejhert - Karolinska Institutet
Yosuke Mizuno - Saitama Medical University
Hiromasa Morikawa - Osaka International University
Mitsuru Morimoto - RIKEN Center for Brain Science
Kazuyo Moro - RIKEN Center for Integrative Medical Sciences
Kelly J. Morris - Max Delbrück Center for Molecular Medicine
Hozumi Motohashi - Tohoku University
Christine L. Mummery - Leiden University
Yutaka Nakachi - College Station Medical Center
Fumio Nakahara - The University of Tokyo
Toshiyuki Nakamura - The University of Tokyo
Yukio Nakamura - RIKEN
Tadasuke Nozaki - Supreme Council Of Health
Soichi Ogishima - Tohoku University
Naganari Ohkura - Osaka University
Hiroshi Ohno - RIKEN
Mitsuhiro Ohshima - Ohu University
Mariko Okada-Hatakeyama - RIKEN
Yasushi Okazaki - College Station Medical Center
Valerio Orlando - IRCCS Fdn Santa Lucia, Via Fosso di Fiorano 64, I-00143 Rome, Italy
Dmitry A. Ovchinnikov - University of Queensland
Robert Passier - Leiden University
Margaret Patrikakis - Univ New S Wales, Ctr Vasc Res, Sydney, NSW 2052, Australia
Ana Pombo - College Station Medical Center
Swati Pradhan-Bhatt - University of Delaware
Xian-Yang Qin - RIKEN
Michael Rehli - College Station Medical Center
Patrizia Rizzu - German Ctr Neurodegenerat Dis DZNE Tubingen, Otfried Muller Str 23, D-72076 Tubingen, Germany
Sugata Roy - RIKEN
Antti Sajantila - University of Helsinki
Shimon Sakaguchi - Osaka University
Hiroki Sato - The University of Tokyo
Hironori Satoh - Tohoku University
Suzana Savvi - University of Cape Town
Alka Saxena - RIKEN
Christian Schmidl - College Station Medical Center
Claudio Schneider - Centro de Investigaciones Biológicas Margarita Salas
Gundula G. Schulze-Tanzil - Charité - Universitätsmedizin Berlin
Anita Schwegmann - University of Cape Town
Guojun Sheng - Kumamoto University
Jay W. Shin - RIKEN
Daisuke Sugiyama - Kyushu University
Takaaki Sugiyama - The University of Tokyo
Kim M. Summers - University of Edinburgh
Naoko Takahashi - RIKEN
Jun Takai - Tohoku University
Hiroshi Tanaka - College Station Medical Center
Hideki Tatsukawa - Nagoya University
Andru Tomoiu - University of Edinburgh
Hiroo Toyoda - Tohoku University
Marc van de Wetering - Royal Netherlands Acad Arts & Sci, Hubrecht Inst, Uppsalalaan 8, NL-3584 CT Utrecht, Netherlands
Linda M. van den Berg - University of Amsterdam
Roberto Verardo - LNCIB, Padriciano 99, I-34149 Trieste, Italy
Dipti Vijayan - College Station Medical Center
Christine A. Wells - University of Melbourne
Louise N. Winteringham - College Station Medical Center
Ernst Wolvetang - University of Queensland
Yoko Yamaguchi - Nihon University
Masayuki Yamamoto - Tohoku University
Chiyo Yanagi-Mizuochi - Kyushu University
Misako Yoneda - The University of Tokyo
Yohei Yonekura - RIKEN
Peter G. Zhang - University of British Columbia
Silvia Zucchelli - SISSA, Neurosci, Via Bonomea 265, I-34136 Trieste, Italy
Imad Abugessaisa - RIKEN
Erik Arner - RIKEN
Jayson Harshbarger - RIKEN
Atsushi Kondo - RIKEN
Timo Lassmann - RIKEN
Marina Lizio - RIKEN
Serkan Sahin - RIKEN
Thierry Sengstag - RIKEN
Jessica Severin - RIKEN
Hisashi Shimoji - RIKEN
Masanori Suzuki - RIKEN
Harukazu Suzuki - RIKEN
Jun Kawai - RIKEN
Naoto Kondo - RIKEN
Masayoshi Itoh - RIKEN
Carsten O. Daub - RIKEN
Takeya Kasukawa - RIKEN
Hideya Kawaji - RIKEN
Piero Carninci - RIKEN
Alistair R. R. Forrest - RIKEN
Yoshihide Hayashizaki - RIKEN
Publication Details: Scientific data, Vol.4
Publisher: NATURE PORTFOLIO
Number of pages: 10
Grant note: BBS/E/D/20241863; BBS/E/D/20211551; BB/H008098/1; BBS/E/D/20211552; BBS/E/D/20221657; BBS/E/D/20211550; BBS/E/D/10002070 / Biotechnology and Biological Sciences Research Council; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) MC_U120061476 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) 103258/Z/13/Z / Wellcome Trust MC_U120061476 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan BBS/E/D/20241863; BB/H008098/1; BBS/E/D/20211550; BBS/E/D/20211552; BBS/E/D/20211551; BBS/E/D/20221657 / BBSRC; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) MEXT, Japan; Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT) MEXT; Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT) 15K08539; 16K00385; 15H04744; 16K07372 / Grants-in-Aid for Scientific Research; Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT); Japan Society for the Promotion of Science; Grants-in-Aid for Scientific Research (KAKENHI)
Identifiers: 9941827808331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article