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 Babina; J. 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

doi:10.1038/sdata.2017.112

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

King Abdullah University of Science and Technology

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

74 Scopus citations

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 language	English (US)
Journal	Scientific data
Volume	4
Issue number	1
DOIs	https://doi.org/10.1038/sdata.2017.112
State	Published - Aug 29 2017

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10.1038/sdata.2017.112

https://repository.kaust.edu.sa/bitstream/10754/625836/1/sdata2017112.pdf

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Noguchi, S., Arakawa, T., Fukuda, S., Furuno, M., Hasegawa, A., Hori, F., Ishikawa-Kato, S., Kaida, K., Kaiho, A., Kanamori-Katayama, M., Kawashima, T., Sakai, M., Simon, C., Suzuki, N., Tagami, M., Watanabe, S., Yoshida, S., Arner, P., Axton, R. A., ... Saka, A. (2017). FANTOM5 CAGE profiles of human and mouse samples. Scientific data, 4(1). https://doi.org/10.1038/sdata.2017.112

Noguchi, Shuhei ; Arakawa, Takahiro ; Fukuda, Shiro ; Furuno, Masaaki ; Hasegawa, Akira ; Hori, Fumi ; Ishikawa-Kato, Sachi ; Kaida, Kaoru ; Kaiho, Ai ; Kanamori-Katayama, Mutsumi ; Kawashima, Tsugumi ; Sakai, Mizuho ; Simon, Christophe ; Suzuki, Naoko ; Tagami, Michihira ; Watanabe, Shoko ; Yoshida, Shigehiro ; Arner, Peter ; Axton, Richard A. ; Babina, Magda ; Baillie, J. Kenneth ; Mummery, Christine L. ; Barnett, Timothy C. ; Beckhouse, Anthony G. ; Blumenthal, Antje ; Bodega, Beatrice ; Bonetti, Alessandro ; Briggs, James ; Brombacher, Frank ; Carlisle, Ailsa J. ; Clevers, Hans C. ; Davis, Carrie A. ; Nakachi, Yutaka ; Detmar, Michael ; Dohi, Taeko ; Edge, Albert S.B. ; Edinger, Matthias ; Ehrlund, Anna ; Ekwall, Karl ; Endoh, Mitsuhiro ; Enomoto, Hideki ; Eslami, Afsaneh ; Fagiolini, Michela ; Nakahara, Fumio ; Fairbairn, Lynsey ; Farach-Carson, Mary C. ; Faulkner, Geoffrey J. ; Ferrai, Carmelo ; Fisher, Malcolm E. ; Forrester, Lesley M. ; Fujita, Rie ; Furusawa, Jun-ichi ; Geijtenbeek, Teunis B. ; Gingeras, Thomas ; Nakamura, Toshiyuki ; Goldowitz, Daniel ; Guhl, Sven ; Guler, Reto ; Gustincich, Stefano ; Ha, Thomas J. ; Hamaguchi, Masahide ; Hara, Mitsuko ; Hasegawa, Yuki ; Herlyn, Meenhard ; Heutink, Peter ; Nakamura, Yukio ; Hitchens, Kelly J. ; Hume, David A. ; Ikawa, Tomokatsu ; Orlando, Valerio ; Kai, Chieko ; Kawamoto, Hiroshi ; Kawamura, Yuki I. ; Kempfle, Judith S. ; Kenna, Tony J. ; Kere, Juha ; Nozaki, Tadasuke ; Khachigian, Levon M. ; Kitamura, Toshio ; Klein, Sarah ; Klinken, S. Peter ; Knox, Alan J. ; Kojima, Soichi ; Koseki, Haruhiko ; Koyasu, Shigeo ; Lee, Weonju ; Lennartsson, Andreas ; Ogishima, Soichi ; Mackay-sim, Alan ; Mejhert, Niklas ; Mizuno, Yosuke ; Morikawa, Hiromasa ; Morimoto, Mitsuru ; Moro, Kazuyo ; Morris, Kelly J. ; Motohashi, Hozumi ; Ohkura, Naganari ; Ohno, Hiroshi ; Ohshima, Mitsuhiro ; Kojima, Miki ; Okada-Hatakeyama, Mariko ; Okazaki, Yasushi ; Orlando, Valerio ; Ovchinnikov, Dmitry A. ; Passier, Robert ; Patrikakis, Margaret ; Pombo, Ana ; Pradhan-Bhatt, Swati ; Qin, Xian-Yang ; Rehli, Michael ; Kubosaki, Atsutaka ; Rizzu, Patrizia ; Roy, Sugata ; Sajantila, Antti ; Sakaguchi, Shimon ; Sato, Hiroki ; Satoh, Hironori ; Savvi, Suzana ; Saxena, Alka ; Schmidl, Christian ; Schneider, Claudio ; Manabe, Ri-ichiroh ; Schulze-Tanzil, Gundula G. ; Schwegmann, Anita ; Sheng, Guojun ; Shin, Jay W. ; Sugiyama, Daisuke ; Sugiyama, Takaaki ; Summers, Kim M. ; Takahashi, Naoko ; Takai, Jun ; Tanaka, Hiroshi ; Murata, Mitsuyoshi ; Tatsukawa, Hideki ; Tomoiu, Andru ; Toyoda, Hiroo ; van de Wetering, Marc ; van den Berg, Linda M. ; Verardo, Roberto ; Vijayan, Dipti ; Wells, Christine A. ; Winteringham, Louise N. ; Wolvetang, Ernst ; Nagao-Sato, Sayaka ; Yamaguchi, Yoko ; Yamamoto, Masayuki ; Yanagi-Mizuochi, Chiyo ; Yoneda, Misako ; Yonekura, Yohei ; Zhang, Peter G. ; Zucchelli, Silvia ; Abugessaisa, Imad ; Arner, Erik ; Harshbarger, Jayson ; Nakazato, Kenichi ; Kondo, Atsushi ; Lassmann, Timo ; Lizio, Marina ; Sahin, Serkan ; Sengstag, Thierry ; Severin, Jessica ; Shimoji, Hisashi ; Suzuki, Masanori ; Suzuki, Harukazu ; Kawai, Jun ; Ninomiya, Noriko ; Kondo, Naoto ; Itoh, Masayoshi ; Daub, Carsten O. ; Kasukawa, Takeya ; Kawaji, Hideya ; Carninci, Piero ; Forrest, Alistair R.R. ; Hayashizaki, Yoshihide ; Nishiyori-Sueki, Hiromi ; Noma, Shohei ; Saijyo, Eri ; Saka, Akiko. / FANTOM5 CAGE profiles of human and mouse samples. In: Scientific data. 2017 ; Vol. 4, No. 1.

@article{882033c61f3c42c5b0ae882449f683a4,

title = "FANTOM5 CAGE profiles of human and mouse samples",

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.",

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

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: FANTOM5 was made possible by a Research Grant for RIKEN Omics Science Center from MEXT to Y.H. and a grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Y.H. It was also supported by Research Grants for RIKEN Preventive Medicine and Diagnosis Innovation Program to Y.H. and RIKEN Centre for Life Science Technologies, Division of Genomic Technologies (from the MEXT, Japan).",

year = "2017",

month = aug,

day = "29",

doi = "10.1038/sdata.2017.112",

language = "English (US)",

volume = "4",

journal = "Scientific data",

issn = "2052-4463",

publisher = "Nature Publishing Group",

number = "1",

}

Noguchi, S, Arakawa, T, Fukuda, S, Furuno, M, Hasegawa, A, Hori, F, Ishikawa-Kato, S, Kaida, K, Kaiho, A, Kanamori-Katayama, M, Kawashima, T, Sakai, M, Simon, C, Suzuki, N, Tagami, M, Watanabe, S, Yoshida, S, Arner, P, Axton, RA, Babina, M, Baillie, JK, Mummery, CL, Barnett, TC, Beckhouse, AG, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Carlisle, AJ, Clevers, HC, Davis, CA, Nakachi, Y, Detmar, M, Dohi, T, Edge, ASB, Edinger, M, Ehrlund, A, Ekwall, K, Endoh, M, Enomoto, H, Eslami, A, Fagiolini, M, Nakahara, F, Fairbairn, L, Farach-Carson, MC, Faulkner, GJ, Ferrai, C, Fisher, ME, Forrester, LM, Fujita, R, Furusawa, J, Geijtenbeek, TB, Gingeras, T, Nakamura, T, Goldowitz, D, Guhl, S, Guler, R, Gustincich, S, Ha, TJ, Hamaguchi, M, Hara, M, Hasegawa, Y, Herlyn, M, Heutink, P, Nakamura, Y, Hitchens, KJ, Hume, DA, Ikawa, T, Orlando, V, Kai, C, Kawamoto, H, Kawamura, YI, Kempfle, JS, Kenna, TJ, Kere, J, Nozaki, T, Khachigian, LM, Kitamura, T, Klein, S, Klinken, SP, Knox, AJ, Kojima, S, Koseki, H, Koyasu, S, Lee, W, Lennartsson, A, Ogishima, S, Mackay-sim, A, Mejhert, N, Mizuno, Y, Morikawa, H, Morimoto, M, Moro, K, Morris, KJ, Motohashi, H, Ohkura, N, Ohno, H, Ohshima, M, Kojima, M, Okada-Hatakeyama, M, Okazaki, Y, Orlando, V, Ovchinnikov, DA, Passier, R, Patrikakis, M, Pombo, A, Pradhan-Bhatt, S, Qin, X-Y, Rehli, M, Kubosaki, A, Rizzu, P, Roy, S, Sajantila, A, Sakaguchi, S, Sato, H, Satoh, H, Savvi, S, Saxena, A, Schmidl, C, Schneider, C, Manabe, R, Schulze-Tanzil, GG, Schwegmann, A, Sheng, G, Shin, JW, Sugiyama, D, Sugiyama, T, Summers, KM, Takahashi, N, Takai, J, Tanaka, H, Murata, M, Tatsukawa, H, Tomoiu, A, Toyoda, H, van de Wetering, M, van den Berg, LM, Verardo, R, Vijayan, D, Wells, CA, Winteringham, LN, Wolvetang, E, Nagao-Sato, S, Yamaguchi, Y, Yamamoto, M, Yanagi-Mizuochi, C, Yoneda, M, Yonekura, Y, Zhang, PG, Zucchelli, S, Abugessaisa, I, Arner, E, Harshbarger, J, Nakazato, K, Kondo, A, Lassmann, T, Lizio, M, Sahin, S, Sengstag, T, Severin, J, Shimoji, H, Suzuki, M, Suzuki, H, Kawai, J, Ninomiya, N, Kondo, N, Itoh, M, Daub, CO, Kasukawa, T, Kawaji, H, Carninci, P, Forrest, ARR, Hayashizaki, Y, Nishiyori-Sueki, H, Noma, S, Saijyo, E & Saka, A 2017, 'FANTOM5 CAGE profiles of human and mouse samples', Scientific data, vol. 4, no. 1. https://doi.org/10.1038/sdata.2017.112

FANTOM5 CAGE profiles of human and mouse samples. / Noguchi, Shuhei; Arakawa, Takahiro; Fukuda, Shiro; Furuno, Masaaki; Hasegawa, Akira; Hori, Fumi; Ishikawa-Kato, Sachi; Kaida, Kaoru; Kaiho, Ai; Kanamori-Katayama, Mutsumi; Kawashima, Tsugumi; Sakai, Mizuho; Simon, Christophe; Suzuki, Naoko; Tagami, Michihira; Watanabe, Shoko; Yoshida, Shigehiro; Arner, Peter; Axton, Richard A.; Babina, Magda; Baillie, J. Kenneth; Mummery, Christine L.; Barnett, Timothy C.; Beckhouse, Anthony G.; Blumenthal, Antje; Bodega, Beatrice; Bonetti, Alessandro; Briggs, James; Brombacher, Frank; Carlisle, Ailsa J.; Clevers, Hans C.; Davis, Carrie A.; Nakachi, Yutaka; Detmar, Michael; Dohi, Taeko; Edge, Albert S.B.; Edinger, Matthias; Ehrlund, Anna; Ekwall, Karl; Endoh, Mitsuhiro; Enomoto, Hideki; Eslami, Afsaneh; Fagiolini, Michela; Nakahara, Fumio; Fairbairn, Lynsey; Farach-Carson, Mary C.; Faulkner, Geoffrey J.; Ferrai, Carmelo; Fisher, Malcolm E.; Forrester, Lesley M.; Fujita, Rie; Furusawa, Jun-ichi; Geijtenbeek, Teunis B.; Gingeras, Thomas; Nakamura, Toshiyuki; Goldowitz, Daniel; Guhl, Sven; Guler, Reto; Gustincich, Stefano; Ha, Thomas J.; Hamaguchi, Masahide; Hara, Mitsuko; Hasegawa, Yuki; Herlyn, Meenhard; Heutink, Peter; Nakamura, Yukio; Hitchens, Kelly J.; Hume, David A.; Ikawa, Tomokatsu; Orlando, Valerio; Kai, Chieko; Kawamoto, Hiroshi; Kawamura, Yuki I.; Kempfle, Judith S.; Kenna, Tony J.; Kere, Juha; Nozaki, Tadasuke; Khachigian, Levon M.; Kitamura, Toshio; Klein, Sarah; Klinken, S. Peter; Knox, Alan J.; Kojima, Soichi; Koseki, Haruhiko; Koyasu, Shigeo; Lee, Weonju; Lennartsson, Andreas; Ogishima, Soichi; Mackay-sim, Alan; Mejhert, Niklas; Mizuno, Yosuke; Morikawa, Hiromasa; Morimoto, Mitsuru; Moro, Kazuyo; Morris, Kelly J.; Motohashi, Hozumi; Ohkura, Naganari; Ohno, Hiroshi; Ohshima, Mitsuhiro; Kojima, Miki; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry A.; Passier, Robert; Patrikakis, Margaret; Pombo, Ana; Pradhan-Bhatt, Swati; Qin, Xian-Yang; Rehli, Michael; Kubosaki, Atsutaka; Rizzu, Patrizia; Roy, Sugata; Sajantila, Antti; Sakaguchi, Shimon; Sato, Hiroki; Satoh, Hironori; Savvi, Suzana; Saxena, Alka; Schmidl, Christian; Schneider, Claudio; Manabe, Ri-ichiroh; Schulze-Tanzil, Gundula G.; Schwegmann, Anita; Sheng, Guojun; Shin, Jay W.; Sugiyama, Daisuke; Sugiyama, Takaaki; Summers, Kim M.; Takahashi, Naoko; Takai, Jun; Tanaka, Hiroshi; Murata, Mitsuyoshi; Tatsukawa, Hideki; Tomoiu, Andru; Toyoda, Hiroo; van de Wetering, Marc; van den Berg, Linda M.; Verardo, Roberto; Vijayan, Dipti; Wells, Christine A.; Winteringham, Louise N.; Wolvetang, Ernst; Nagao-Sato, Sayaka; Yamaguchi, Yoko; Yamamoto, Masayuki; Yanagi-Mizuochi, Chiyo; Yoneda, Misako; Yonekura, Yohei; Zhang, Peter G.; Zucchelli, Silvia; Abugessaisa, Imad; Arner, Erik; Harshbarger, Jayson; Nakazato, Kenichi; Kondo, Atsushi; Lassmann, Timo; Lizio, Marina; Sahin, Serkan; Sengstag, Thierry; Severin, Jessica; Shimoji, Hisashi; Suzuki, Masanori; Suzuki, Harukazu; Kawai, Jun; Ninomiya, Noriko; Kondo, Naoto; Itoh, Masayoshi; Daub, Carsten O.; Kasukawa, Takeya; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair R.R.; Hayashizaki, Yoshihide; Nishiyori-Sueki, Hiromi; Noma, Shohei; Saijyo, Eri; Saka, Akiko.

In: Scientific data, Vol. 4, No. 1, 29.08.2017.

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

TY - JOUR

T1 - FANTOM5 CAGE profiles of human and mouse samples

AU - Noguchi, Shuhei

AU - Arakawa, Takahiro

AU - Fukuda, Shiro

AU - Furuno, Masaaki

AU - Hasegawa, Akira

AU - Hori, Fumi

AU - Ishikawa-Kato, Sachi

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N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: FANTOM5 was made possible by a Research Grant for RIKEN Omics Science Center from MEXT to Y.H. and a grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Y.H. It was also supported by Research Grants for RIKEN Preventive Medicine and Diagnosis Innovation Program to Y.H. and RIKEN Centre for Life Science Technologies, Division of Genomic Technologies (from the MEXT, Japan).

PY - 2017/8/29

Y1 - 2017/8/29

N2 - 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.

AB - 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.

UR - http://hdl.handle.net/10754/625836

UR - https://www.nature.com/articles/sdata2017112

UR - http://www.scopus.com/inward/record.url?scp=85028461506&partnerID=8YFLogxK

U2 - 10.1038/sdata.2017.112

DO - 10.1038/sdata.2017.112

M3 - Article

C2 - 28850106

VL - 4

JO - Scientific data

JF - Scientific data

SN - 2052-4463

IS - 1

ER -

FANTOM5 CAGE profiles of human and mouse samples

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