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, Mizuho Sakai, Christophe Simon, Naoko Suzuki, Michihira Tagami, Shoko Watanabe, Shigehiro Yoshida, Peter Arner, Richard A. Axton, Magda BabinaJ. Kenneth Baillie, Christine L. Mummery, 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, Yutaka Nakachi, Michael Detmar, Taeko Dohi, Albert S.B. Edge, Matthias Edinger, Anna Ehrlund, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Afsaneh Eslami, Michela Fagiolini, Fumio Nakahara, 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, Toshiyuki Nakamura, Daniel Goldowitz, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Yuki Hasegawa, Meenhard Herlyn, Peter Heutink, Yukio Nakamura, Kelly J. Hitchens, David A. Hume, Tomokatsu Ikawa, Valerio Orlando, Chieko Kai, Hiroshi Kawamoto, Yuki I. Kawamura, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Tadasuke Nozaki, Levon M. Khachigian, Toshio Kitamura, Sarah Klein, S. Peter Klinken, Alan J. Knox, Soichi Kojima, Haruhiko Koseki, Shigeo Koyasu, Weonju Lee, Andreas Lennartsson, Soichi Ogishima, Alan Mackay-sim, Niklas Mejhert, Yosuke Mizuno, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Kelly J. Morris, Hozumi Motohashi, Naganari Ohkura, Hiroshi Ohno, Mitsuhiro Ohshima, Miki Kojima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Robert Passier, Margaret Patrikakis, Ana Pombo, Swati Pradhan-Bhatt, Xian-Yang Qin, Michael Rehli, Atsutaka Kubosaki, Patrizia Rizzu, Sugata Roy, Antti Sajantila, Shimon Sakaguchi, Hiroki Sato, Hironori Satoh, Suzana Savvi, Alka Saxena, Christian Schmidl, Claudio Schneider, Ri-ichiroh Manabe, Gundula G. Schulze-Tanzil, Anita Schwegmann, Guojun Sheng, Jay W. Shin, Daisuke Sugiyama, Takaaki Sugiyama, Kim M. Summers, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Mitsuyoshi Murata, 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, Sayaka Nagao-Sato, Yoko Yamaguchi, Masayuki Yamamoto, Chiyo Yanagi-Mizuochi, Misako Yoneda, Yohei Yonekura, Peter G. Zhang, Silvia Zucchelli, Imad Abugessaisa, Erik Arner, Jayson Harshbarger, Kenichi Nakazato, Atsushi Kondo, Timo Lassmann, Marina Lizio, Serkan Sahin, Thierry Sengstag, Jessica Severin, Hisashi Shimoji, Masanori Suzuki, Harukazu Suzuki, Jun Kawai, Noriko Ninomiya, Naoto Kondo, Masayoshi Itoh, Carsten O. Daub, Takeya Kasukawa, Hideya Kawaji, Piero Carninci, Alistair R.R. Forrest, Yoshihide Hayashizaki, Hiromi Nishiyori-Sueki, Shohei Noma, Eri Saijyo, Akiko Saka

Research output: Contribution to journal › Article › peer-review

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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.
Original languageEnglish (US)
JournalScientific data
Volume4
Issue number1
DOIs
StatePublished - Aug 29 2017

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  • FANTOM5 CAGE profiles of human and mouse samples

    Noguchi, S. (Creator), Arakawa, T. (Creator), Fukuda, S. (Creator), Furuno, M. (Creator), Hasegawa, A. (Creator), Hori, F. (Creator), Ishikawa-Kato, S. (Creator), Kaida, K. (Creator), Kaiho, A. (Creator), Kanamori-Katayama, M. (Creator), Kawashima, T. (Creator), Kojima, M. (Creator), Kubosaki, A. (Creator), Manabe, R. (Creator), Murata, M. (Creator), Nagao-Sato, S. (Creator), Nakazato, K. (Creator), Ninomiya, N. (Creator), Nishiyori-Sueki, H. (Creator), Noma, S. (Creator), Saijyo, E. (Creator), Saka, A. (Creator), Sakai, M. (Creator), Simon, C. (Creator), Suzuki, N. (Creator), Tagami, M. (Creator), Watanabe, S. (Creator), Yoshida, S. (Creator), Arner, P. (Creator), Axton, R. A. (Creator), Babina, M. (Creator), Baillie, J. K. (Creator), Barnett, T. C. (Creator), Beckhouse, A. G. (Creator), Blumenthal, A. (Creator), Bodega, B. (Creator), Bonetti, A. (Creator), Briggs, J. (Creator), Brombacher, F. (Creator), Carlisle, A. J. (Creator), Clevers, H. C. (Creator), Davis, C. A. (Creator), Detmar, M. (Creator), Dohi, T. (Creator), Edge, A. S. B. (Creator), Edinger, M. (Creator), Ehrlund, A. (Creator), Ekwall, K. (Creator), Endoh, M. (Creator), Enomoto, H. (Creator), Eslami, A. (Creator), Fagiolini, M. (Creator), Fairbairn, L. (Creator), Farach-Carson, M. C. (Creator), Faulkner, G. J. (Creator), Ferrai, C. (Creator), Fisher, M. E. (Creator), Forrester, L. M. (Creator), Fujita, R. (Creator), Furusawa, J. (Creator), Geijtenbeek, T. B. (Creator), Gingeras, T. (Creator), Goldowitz, D. (Creator), Guhl, S. (Creator), Guler, R. (Creator), Gustincich, S. (Creator), Ha, T. J. (Creator), Hamaguchi, M. (Creator), Hara, M. (Creator), Hasegawa, Y. (Creator), Herlyn, M. (Creator), Heutink, P. (Creator), Hitchens, K. J. (Creator), Hume, D. A. (Creator), Ikawa, T. (Creator), Ishizu, Y. (Creator), Kai, C. (Creator), Kawamoto, H. (Creator), Kawamura, Y. I. (Creator), Kempfle, J. S. (Creator), Kenna, T. J. (Creator), Kere, J. (Creator), Khachigian, L. M. (Creator), Kitamura, T. (Creator), Klein, S. (Creator), Klinken, S. P. (Creator), Knox, A. J. (Creator), Kojima, S. (Creator), Koseki, H. (Creator), Koyasu, S. (Creator), Lee, W. (Creator), Lennartsson, A. (Creator), Mackay-sim, A. (Creator), Mejhert, N. (Creator), Mizuno, Y. (Creator), Morikawa, H. (Creator), Morimoto, M. (Creator), Moro, K. (Creator), Morris, K. J. (Creator), Motohashi, H. (Creator), Mummery, C. L. (Creator), Nakachi, Y. (Creator), Nakahara, F. (Creator), Nakamura, T. (Creator), Nakamura, Y. (Creator), Nozaki, T. (Creator), Ogishima, S. (Creator), Ohkura, N. (Creator), Ohno, H. (Creator), Ohshima, M. (Creator), Okada-Hatakeyama, M. (Creator), Okazaki, Y. (Creator), Orlando, V. (Creator), Ovchinnikov, D. A. (Creator), Passier, R. (Creator), Patrikakis, M. (Creator), Pombo, A. (Creator), Pradhan-Bhatt, S. (Creator), Qin, X. (Creator), Rehli, M. (Creator), Rizzu, P. (Creator), Roy, S. (Creator), Sajantila, A. (Creator), Sakaguchi, S. (Creator), Sato, H. (Creator), Satoh, H. (Creator), Savvi, S. (Creator), Saxena, A. (Creator), Schmidl, C. (Creator), Schneider, C. (Creator), Schulze-Tanzil, G. G. (Creator), Schwegmann, A. (Creator), Sheng, G. (Creator), Shin, J. W. (Creator), Sugiyama, D. (Creator), Sugiyama, T. (Creator), Summers, K. M. (Creator), Takahashi, N. (Creator), Takai, J. (Creator), Tanaka, H. (Creator), Tatsukawa, H. (Creator), Tomoiu, A. (Creator), Toyoda, H. (Creator), van de Wetering, M. (Creator), van den Berg, L. M. (Creator), Verardo, R. (Creator), Vijayan, D. (Creator), Wells, C. A. (Creator), Winteringham, L. N. (Creator), Wolvetang, E. (Creator), Yamaguchi, Y. (Creator), Yamamoto, M. (Creator), Yanagi-Mizuochi, C. (Creator), Yoneda, M. (Creator), Yonekura, Y. (Creator), Zhang, P. G. (Creator), Zucchelli, S. (Creator), Abugessaisa, I. (Creator), Arner, E. (Creator), Harshbarger, J. (Creator), Kondo, A. (Creator), Lassmann, T. (Creator), Lizio, M. (Creator), Sahin, S. (Creator), Sengstag, T. (Creator), Severin, J. (Creator), Shimoji, H. (Creator), Suzuki, M. (Creator), Suzuki, H. (Creator), Kawai, J. (Creator), Kondo, N. (Creator), Itoh, M. (Creator), Daub, C. O. (Creator), Kasukawa, T. (Creator), Kawaji, H. (Creator), Carninci, P. (Creator), Forrest, A. R. R. (Creator), Hayashizaki, Y. (Creator), Noguchi, S. (Creator), Arakawa, T. (Creator), Fukuda, S. (Creator), Furuno, M. (Creator), Hasegawa, A. (Creator), Hori, F. (Creator), Ishikawa-Kato, S. (Creator), Kaida, K. (Creator), Kaiho, A. (Creator), Kanamori-Katayama, M. (Creator), Kawashima, T. (Creator), Kojima, M. (Creator), Kubosaki, A. (Creator), Manabe, R. (Creator), Murata, M. (Creator), Nagao-Sato, S. (Creator), Nakazato, K. (Creator), Ninomiya, N. (Creator), Nishiyori-Sueki, H. (Creator), Noma, S. (Creator), Saijyo, E. (Creator), Saka, A. (Creator), Sakai, M. (Creator), Simon, C. (Creator), Suzuki, N. (Creator), Tagami, M. (Creator), Watanabe, S. (Creator), Yoshida, S. (Creator), Arner, P. (Creator), Axton, R. A. (Creator), Babina, M. (Creator), Baillie, J. K. (Creator), Barnett, T. C. (Creator), Beckhouse, A. G. (Creator), Blumenthal, A. (Creator), Bodega, B. (Creator), Bonetti, A. (Creator), Briggs, J. (Creator), Brombacher, F. (Creator), Carlisle, A. J. (Creator), Clevers, H. C. (Creator), Davis, C. A. (Creator), Detmar, M. (Creator), Dohi, T. (Creator), Edge, A. S. B. (Creator), Edinger, M. (Creator), Ehrlund, A. (Creator), Ekwall, K. (Creator), Endoh, M. (Creator), Enomoto, H. (Creator), Eslami, A. (Creator), Fagiolini, M. (Creator), Fairbairn, L. (Creator), Farach-Carson, M. C. (Creator), Faulkner, G. J. (Creator), Ferrai, C. (Creator), Fisher, M. E. (Creator), Forrester, L. M. (Creator), Fujita, R. (Creator), Furusawa, J. (Creator), Geijtenbeek, T. B. (Creator), Gingeras, T. (Creator), Goldowitz, D. (Creator), Guhl, S. (Creator), Guler, R. (Creator), Gustincich, S. (Creator), Ha, T. J. (Creator), Hamaguchi, M. (Creator), Hara, M. (Creator), Hasegawa, Y. (Creator), Herlyn, M. (Creator), Heutink, P. (Creator), Hitchens, K. J. (Creator), Hume, D. A. (Creator), Ikawa, T. (Creator), Ishizu, Y. (Creator), Kai, C. (Creator), Kawamoto, H. (Creator), Kawamura, Y. I. (Creator), Kempfle, J. S. (Creator), Kenna, T. J. (Creator), Kere, J. (Creator), Khachigian, L. M. (Creator), Kitamura, T. (Creator), Klein, S. (Creator), Klinken, S. P. (Creator), Knox, A. J. (Creator), Kojima, S. (Creator), Koseki, H. (Creator), Koyasu, S. (Creator), Lee, W. (Creator), Lennartsson, A. (Creator), Mackay-sim, A. (Creator), Mejhert, N. (Creator), Mizuno, Y. (Creator), Morikawa, H. (Creator), Morimoto, M. (Creator), Moro, K. (Creator), Morris, K. J. (Creator), Motohashi, H. (Creator), Mummery, C. L. (Creator), Nakachi, Y. (Creator), Nakahara, F. (Creator), Nakamura, T. (Creator), Nakamura, Y. (Creator), Nozaki, T. (Creator), Ogishima, S. (Creator), Ohkura, N. (Creator), Ohno, H. (Creator), Ohshima, M. (Creator), Okada-Hatakeyama, M. (Creator), Okazaki, Y. (Creator), Ovchinnikov, D. A. (Creator), Passier, R. (Creator), Patrikakis, M. (Creator), Pombo, A. (Creator), Pradhan-Bhatt, S. (Creator), Qin, X. (Creator), Rehli, M. (Creator), Rizzu, P. (Creator), Roy, S. (Creator), Sajantila, A. (Creator), Sakaguchi, S. (Creator), Sato, H. (Creator), Satoh, H. (Creator), Savvi, S. (Creator), Saxena, A. (Creator), Schmidl, C. (Creator), Schneider, C. (Creator), Schulze-Tanzil, G. G. (Creator), Schwegmann, A. (Creator), Sheng, G. (Creator), Shin, J. W. (Creator), Sugiyama, D. (Creator), Sugiyama, T. (Creator), Summers, K. M. (Creator), Takahashi, N. (Creator), Takai, J. (Creator), Tanaka, H. (Creator), Tatsukawa, H. (Creator), Tomoiu, A. (Creator), Toyoda, H. (Creator), van de Wetering, M. (Creator), van den Berg, L. M. (Creator), Verardo, R. (Creator), Vijayan, D. (Creator), Wells, C. A. (Creator), Winteringham, L. N. (Creator), Wolvetang, E. (Creator), Yamaguchi, Y. (Creator), Yamamoto, M. (Creator), Yanagi-Mizuochi, C. (Creator), Yoneda, M. (Creator), Yonekura, Y. (Creator), Zhang, P. G. (Creator), Zucchelli, S. (Creator), Abugessaisa, I. (Creator), Arner, E. (Creator), Harshbarger, J. (Creator), Kondo, A. (Creator), Lassmann, T. (Creator), Lizio, M. (Creator), Sahin, S. (Creator), Sengstag, T. (Creator), Severin, J. (Creator), Shimoji, H. (Creator), Suzuki, M. (Creator), Suzuki, H. (Creator), Kawai, J. (Creator), Kondo, N. (Creator), Itoh, M. (Creator), Daub, C. O. (Creator), Kasukawa, T. (Creator), Kawaji, H. (Creator), Carninci, P. (Creator), Forrest, A. R. R. (Creator) & Hayashizaki, Y. (Creator), figshare, 2017

    DOI: 10.6084/m9.figshare.c.3728767.v1, http://hdl.handle.net/10754/664213

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