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 & 158 others 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, B. Albert S. 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, Marcvande 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

Research output: Contribution to journalArticle

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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.
LanguageEnglish
Article number170112
JournalScientific Data
Volume4
DOIs
StatePublished - 29 Aug 2017
Externally publishedYes

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Gene Expression Profile
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Mouse
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Cells
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Gene Expression
Genome
Molecules
RNA
Transcriptional Regulation
workflow
Time series
Gene Expression Data
Robotics
Promoter
Chemical activation

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Noguchi, S., Arakawa, T., Fukuda, S., Furuno, M., Hasegawa, A., Hori, F., ... Hayashizaki, Y. (2017). FANTOM5 CAGE profiles of human and mouse samples. Scientific Data, 4, [170112]. DOI: 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 ; Kojima, Miki ; Kubosaki, Atsutaka ; Manabe, Ri Ichiroh ; Murata, Mitsuyoshi ; Nagao-Sato, Sayaka ; Nakazato, Kenichi ; Ninomiya, Noriko ; Nishiyori-Sueki, Hiromi ; Noma, Shohei ; Saijyo, Eri ; Saka, Akiko ; Sakai, Mizuho ; Simon, Christophe ; Suzuki, Naoko ; Tagami, Michihira ; Watanabe, Shoko ; Yoshida, Shigehiro ; Arner, Peter ; Axton, Richard A. ; Babina, Magda ; Kenneth Baillie, J. ; 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. ; Detmar, Michael ; Dohi, Taeko ; Edge, B. Albert S. ; Edinger, Matthias ; Ehrlund, Anna ; Ekwall, Karl ; Endoh, Mitsuhiro ; Enomoto, Hideki ; Eslami, Afsaneh ; Fagiolini, Michela ; 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 ; Goldowitz, Daniel ; Guhl, Sven ; Guler, Reto ; Gustincich, Stefano ; Ha, Thomas J. ; Hamaguchi, Masahide ; Hara, Mitsuko ; Hasegawa, Yuki ; Herlyn, Meenhard ; Heutink, Peter ; Hitchens, Kelly J. ; Hume, David A. ; Ikawa, Tomokatsu ; Ishizu, Yuri ; Kai, Chieko ; Kawamoto, Hiroshi ; Kawamura, Yuki I. ; Kempfle, Judith S. ; Kenna, Tony J. ; Kere, Juha ; Khachigian, Levon M. ; Kitamura, Toshio ; Klein, Sarah ; Peter Klinken, S. ; Knox, Alan J. ; Kojima, Soichi ; Koseki, Haruhiko ; Koyasu, Shigeo ; Lee, Weonju ; Lennartsson, Andreas ; MacKay-Sim, Alan ; Mejhert, Niklas ; Mizuno, Yosuke ; Morikawa, Hiromasa ; Morimoto, Mitsuru ; Moro, Kazuyo ; Morris, Kelly J. ; Motohashi, Hozumi ; Mummery, Christine L. ; Nakachi, Yutaka ; Nakahara, Fumio ; Nakamura, Toshiyuki ; Nakamura, Yukio ; Nozaki, Tadasuke ; Ogishima, Soichi ; Ohkura, Naganari ; Ohno, Hiroshi ; Ohshima, Mitsuhiro ; Okada-Hatakeyama, Mariko ; Okazaki, Yasushi ; Orlando, Valerio ; Ovchinnikov, Dmitry A. ; Passier, Robert ; Patrikakis, Margaret ; Pombo, Ana ; Pradhan-Bhatt, Swati ; Qin, Xian Yang ; Rehli, Michael ; Rizzu, Patrizia ; Roy, Sugata ; Sajantila, Antti ; Sakaguchi, Shimon ; Sato, Hiroki ; Satoh, Hironori ; Savvi, Suzana ; Saxena, Alka ; Schmidl, Christian ; Schneider, Claudio ; Schulze-Tanzil, Gundula G. ; Schwegmann, Anita ; Sheng, Guojun ; Shin, Jay W. ; Sugiyama, Daisuke ; Sugiyama, Takaaki ; Summers, Kim M. ; Takahashi, Naoko ; Takai, Jun ; Tanaka, Hiroshi ; Tatsukawa, Hideki ; Tomoiu, Andru ; Toyoda, Hiroo ; Wetering, Marcvande ; Berg, Linda M.Van Den ; Verardo, Roberto ; Vijayan, DIpti ; Wells, Christine A. ; Winteringham, Louise N. ; Wolvetang, Ernst ; Yamaguchi, Yoko ; Yamamoto, Masayuki ; Yanagi-Mizuochi, Chiyo ; Yoneda, Misako ; Yonekura, Yohei ; Zhang, Peter G. ; Zucchelli, Silvia ; Abugessaisa, Imad ; Arner, Erik ; Harshbarger, Jayson ; Kondo, Atsushi ; Lassmann, Timo ; Lizio, Marina ; Sahin, Serkan ; Sengstag, Thierry ; Severin, Jessica ; Shimoji, Hisashi ; Suzuki, Masanori ; Suzuki, Harukazu ; Kawai, Jun ; Kondo, Naoto ; Itoh, Masayoshi ; Daub, Carsten O. ; Kasukawa, Takeya ; Kawaji, Hideya ; Carninci, Piero ; Forrest, Alistair R.R. ; Hayashizaki, Yoshihide. / FANTOM5 CAGE profiles of human and mouse samples. In: Scientific Data. 2017 ; Vol. 4.
@article{66d4c90b658b46a2a84cb3fcefe6eaac,
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 Miki Kojima and Atsutaka Kubosaki and Manabe, {Ri Ichiroh} and Mitsuyoshi Murata and Sayaka Nagao-Sato and Kenichi Nakazato and Noriko Ninomiya and Hiromi Nishiyori-Sueki and Shohei Noma and Eri Saijyo and Akiko Saka 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 {Kenneth Baillie}, J. 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 Michael Detmar and Taeko Dohi and Edge, {B. Albert S.} and Matthias Edinger and Anna Ehrlund and Karl Ekwall and Mitsuhiro Endoh and Hideki Enomoto and Afsaneh Eslami and Michela Fagiolini 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 Furusawa, {Jun Ichi} and Geijtenbeek, {Teunis B.} and Thomas Gingeras 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 Hitchens, {Kelly J.} and Hume, {David A.} and Tomokatsu Ikawa and Yuri Ishizu and Chieko Kai and Hiroshi Kawamoto and Kawamura, {Yuki I.} and Kempfle, {Judith S.} and Kenna, {Tony J.} and Juha Kere and Khachigian, {Levon M.} and Toshio Kitamura and Sarah Klein and {Peter Klinken}, S. and Knox, {Alan J.} and Soichi Kojima and Haruhiko Koseki and Shigeo Koyasu and Weonju Lee and Andreas Lennartsson 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 Mummery, {Christine L.} and Yutaka Nakachi and Fumio Nakahara and Toshiyuki Nakamura and Yukio Nakamura and Tadasuke Nozaki and Soichi Ogishima and Naganari Ohkura and Hiroshi Ohno and Mitsuhiro Ohshima 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 Qin, {Xian Yang} and Michael Rehli 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 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 Hideki Tatsukawa and Andru Tomoiu and Hiroo Toyoda and Marcvande Wetering and Berg, {Linda M.Van Den} and Roberto Verardo and DIpti Vijayan and Wells, {Christine A.} and Winteringham, {Louise N.} and Ernst Wolvetang 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 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 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",
year = "2017",
month = "8",
day = "29",
doi = "10.1038/sdata.2017.112",
language = "English",
volume = "4",
journal = "Scientific Data",
issn = "2052-4463",
publisher = "Nature Publishing Group",

}

Noguchi, S, Arakawa, T, Fukuda, S, Furuno, M, Hasegawa, A, Hori, F, Ishikawa-Kato, S, Kaida, K, Kaiho, A, Kanamori-Katayama, M, Kawashima, T, Kojima, M, Kubosaki, A, Manabe, RI, Murata, M, Nagao-Sato, S, Nakazato, K, Ninomiya, N, Nishiyori-Sueki, H, Noma, S, Saijyo, E, Saka, A, Sakai, M, Simon, C, Suzuki, N, Tagami, M, Watanabe, S, Yoshida, S, Arner, P, Axton, RA, Babina, M, Kenneth Baillie, J, Barnett, TC, Beckhouse, AG, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Carlisle, AJ, Clevers, HC, Davis, CA, Detmar, M, Dohi, T, Edge, BAS, Edinger, M, Ehrlund, A, Ekwall, K, Endoh, M, Enomoto, H, Eslami, A, Fagiolini, M, Fairbairn, L, Farach-Carson, MC, Faulkner, GJ, Ferrai, C, Fisher, ME, Forrester, LM, Fujita, R, Furusawa, JI, Geijtenbeek, TB, Gingeras, T, Goldowitz, D, Guhl, S, Guler, R, Gustincich, S, Ha, TJ, Hamaguchi, M, Hara, M, Hasegawa, Y, Herlyn, M, Heutink, P, Hitchens, KJ, Hume, DA, Ikawa, T, Ishizu, Y, Kai, C, Kawamoto, H, Kawamura, YI, Kempfle, JS, Kenna, TJ, Kere, J, Khachigian, LM, Kitamura, T, Klein, S, Peter Klinken, S, Knox, AJ, Kojima, S, Koseki, H, Koyasu, S, Lee, W, Lennartsson, A, MacKay-Sim, A, Mejhert, N, Mizuno, Y, Morikawa, H, Morimoto, M, Moro, K, Morris, KJ, Motohashi, H, Mummery, CL, Nakachi, Y, Nakahara, F, Nakamura, T, Nakamura, Y, Nozaki, T, Ogishima, S, Ohkura, N, Ohno, H, Ohshima, M, Okada-Hatakeyama, M, Okazaki, Y, Orlando, V, Ovchinnikov, DA, Passier, R, Patrikakis, M, Pombo, A, Pradhan-Bhatt, S, Qin, XY, Rehli, M, Rizzu, P, Roy, S, Sajantila, A, Sakaguchi, S, Sato, H, Satoh, H, Savvi, S, Saxena, A, Schmidl, C, Schneider, C, Schulze-Tanzil, GG, Schwegmann, A, Sheng, G, Shin, JW, Sugiyama, D, Sugiyama, T, Summers, KM, Takahashi, N, Takai, J, Tanaka, H, Tatsukawa, H, Tomoiu, A, Toyoda, H, Wetering, M, Berg, LMVD, Verardo, R, Vijayan, DI, Wells, CA, Winteringham, LN, Wolvetang, E, Yamaguchi, Y, Yamamoto, M, Yanagi-Mizuochi, C, Yoneda, M, Yonekura, Y, Zhang, PG, Zucchelli, S, Abugessaisa, I, Arner, E, Harshbarger, J, Kondo, A, Lassmann, T, Lizio, M, Sahin, S, Sengstag, T, Severin, J, Shimoji, H, Suzuki, M, Suzuki, H, Kawai, J, Kondo, N, Itoh, M, Daub, CO, Kasukawa, T, Kawaji, H, Carninci, P, Forrest, ARR & Hayashizaki, Y 2017, 'FANTOM5 CAGE profiles of human and mouse samples' Scientific Data, vol 4, 170112. DOI: 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; Kojima, Miki; Kubosaki, Atsutaka; Manabe, Ri Ichiroh; Murata, Mitsuyoshi; Nagao-Sato, Sayaka; Nakazato, Kenichi; Ninomiya, Noriko; Nishiyori-Sueki, Hiromi; Noma, Shohei; Saijyo, Eri; Saka, Akiko; Sakai, Mizuho; Simon, Christophe; Suzuki, Naoko; Tagami, Michihira; Watanabe, Shoko; Yoshida, Shigehiro; Arner, Peter; Axton, Richard A.; Babina, Magda; Kenneth Baillie, J.; 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.; Detmar, Michael; Dohi, Taeko; Edge, B. Albert S.; Edinger, Matthias; Ehrlund, Anna; Ekwall, Karl; Endoh, Mitsuhiro; Enomoto, Hideki; Eslami, Afsaneh; Fagiolini, Michela; 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; Goldowitz, Daniel; Guhl, Sven; Guler, Reto; Gustincich, Stefano; Ha, Thomas J.; Hamaguchi, Masahide; Hara, Mitsuko; Hasegawa, Yuki; Herlyn, Meenhard; Heutink, Peter; Hitchens, Kelly J.; Hume, David A.; Ikawa, Tomokatsu; Ishizu, Yuri; Kai, Chieko; Kawamoto, Hiroshi; Kawamura, Yuki I.; Kempfle, Judith S.; Kenna, Tony J.; Kere, Juha; Khachigian, Levon M.; Kitamura, Toshio; Klein, Sarah; Peter Klinken, S.; Knox, Alan J.; Kojima, Soichi; Koseki, Haruhiko; Koyasu, Shigeo; Lee, Weonju; Lennartsson, Andreas; MacKay-Sim, Alan; Mejhert, Niklas; Mizuno, Yosuke; Morikawa, Hiromasa; Morimoto, Mitsuru; Moro, Kazuyo; Morris, Kelly J.; Motohashi, Hozumi; Mummery, Christine L.; Nakachi, Yutaka; Nakahara, Fumio; Nakamura, Toshiyuki; Nakamura, Yukio; Nozaki, Tadasuke; Ogishima, Soichi; Ohkura, Naganari; Ohno, Hiroshi; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry A.; Passier, Robert; Patrikakis, Margaret; Pombo, Ana; Pradhan-Bhatt, Swati; Qin, Xian Yang; Rehli, Michael; Rizzu, Patrizia; Roy, Sugata; Sajantila, Antti; Sakaguchi, Shimon; Sato, Hiroki; Satoh, Hironori; Savvi, Suzana; Saxena, Alka; Schmidl, Christian; Schneider, Claudio; Schulze-Tanzil, Gundula G.; Schwegmann, Anita; Sheng, Guojun; Shin, Jay W.; Sugiyama, Daisuke; Sugiyama, Takaaki; Summers, Kim M.; Takahashi, Naoko; Takai, Jun; Tanaka, Hiroshi; Tatsukawa, Hideki; Tomoiu, Andru; Toyoda, Hiroo; Wetering, Marcvande; Berg, Linda M.Van Den; Verardo, Roberto; Vijayan, DIpti; Wells, Christine A.; Winteringham, Louise N.; Wolvetang, Ernst; Yamaguchi, Yoko; Yamamoto, Masayuki; Yanagi-Mizuochi, Chiyo; Yoneda, Misako; Yonekura, Yohei; Zhang, Peter G.; Zucchelli, Silvia; Abugessaisa, Imad; Arner, Erik; Harshbarger, Jayson; Kondo, Atsushi; Lassmann, Timo; Lizio, Marina; Sahin, Serkan; Sengstag, Thierry; Severin, Jessica; Shimoji, Hisashi; Suzuki, Masanori; Suzuki, Harukazu; Kawai, Jun; Kondo, Naoto; Itoh, Masayoshi; Daub, Carsten O.; Kasukawa, Takeya; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair R.R.; Hayashizaki, Yoshihide.

In: Scientific Data, Vol. 4, 170112, 29.08.2017.

Research output: Contribution to journalArticle

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

AU - Kaida,Kaoru

AU - Kaiho,Ai

AU - Kanamori-Katayama,Mutsumi

AU - Kawashima,Tsugumi

AU - Kojima,Miki

AU - Kubosaki,Atsutaka

AU - Manabe,Ri Ichiroh

AU - Murata,Mitsuyoshi

AU - Nagao-Sato,Sayaka

AU - Nakazato,Kenichi

AU - Ninomiya,Noriko

AU - Nishiyori-Sueki,Hiromi

AU - Noma,Shohei

AU - Saijyo,Eri

AU - Saka,Akiko

AU - Sakai,Mizuho

AU - Simon,Christophe

AU - Suzuki,Naoko

AU - Tagami,Michihira

AU - Watanabe,Shoko

AU - Yoshida,Shigehiro

AU - Arner,Peter

AU - Axton,Richard A.

AU - Babina,Magda

AU - Kenneth Baillie,J.

AU - Barnett,Timothy C.

AU - Beckhouse,Anthony G.

AU - Blumenthal,Antje

AU - Bodega,Beatrice

AU - Bonetti,Alessandro

AU - Briggs,James

AU - Brombacher,Frank

AU - Carlisle,Ailsa J.

AU - Clevers,Hans C.

AU - Davis,Carrie A.

AU - Detmar,Michael

AU - Dohi,Taeko

AU - Edge,B. Albert S.

AU - Edinger,Matthias

AU - Ehrlund,Anna

AU - Ekwall,Karl

AU - Endoh,Mitsuhiro

AU - Enomoto,Hideki

AU - Eslami,Afsaneh

AU - Fagiolini,Michela

AU - Fairbairn,Lynsey

AU - Farach-Carson,Mary C.

AU - Faulkner,Geoffrey J.

AU - Ferrai,Carmelo

AU - Fisher,Malcolm E.

AU - Forrester,Lesley M.

AU - Fujita,Rie

AU - Furusawa,Jun Ichi

AU - Geijtenbeek,Teunis B.

AU - Gingeras,Thomas

AU - Goldowitz,Daniel

AU - Guhl,Sven

AU - Guler,Reto

AU - Gustincich,Stefano

AU - Ha,Thomas J.

AU - Hamaguchi,Masahide

AU - Hara,Mitsuko

AU - Hasegawa,Yuki

AU - Herlyn,Meenhard

AU - Heutink,Peter

AU - Hitchens,Kelly J.

AU - Hume,David A.

AU - Ikawa,Tomokatsu

AU - Ishizu,Yuri

AU - Kai,Chieko

AU - Kawamoto,Hiroshi

AU - Kawamura,Yuki I.

AU - Kempfle,Judith S.

AU - Kenna,Tony J.

AU - Kere,Juha

AU - Khachigian,Levon M.

AU - Kitamura,Toshio

AU - Klein,Sarah

AU - Peter Klinken,S.

AU - Knox,Alan J.

AU - Kojima,Soichi

AU - Koseki,Haruhiko

AU - Koyasu,Shigeo

AU - Lee,Weonju

AU - Lennartsson,Andreas

AU - MacKay-Sim,Alan

AU - Mejhert,Niklas

AU - Mizuno,Yosuke

AU - Morikawa,Hiromasa

AU - Morimoto,Mitsuru

AU - Moro,Kazuyo

AU - Morris,Kelly J.

AU - Motohashi,Hozumi

AU - Mummery,Christine L.

AU - Nakachi,Yutaka

AU - Nakahara,Fumio

AU - Nakamura,Toshiyuki

AU - Nakamura,Yukio

AU - Nozaki,Tadasuke

AU - Ogishima,Soichi

AU - Ohkura,Naganari

AU - Ohno,Hiroshi

AU - Ohshima,Mitsuhiro

AU - Okada-Hatakeyama,Mariko

AU - Okazaki,Yasushi

AU - Orlando,Valerio

AU - Ovchinnikov,Dmitry A.

AU - Passier,Robert

AU - Patrikakis,Margaret

AU - Pombo,Ana

AU - Pradhan-Bhatt,Swati

AU - Qin,Xian Yang

AU - Rehli,Michael

AU - Rizzu,Patrizia

AU - Roy,Sugata

AU - Sajantila,Antti

AU - Sakaguchi,Shimon

AU - Sato,Hiroki

AU - Satoh,Hironori

AU - Savvi,Suzana

AU - Saxena,Alka

AU - Schmidl,Christian

AU - Schneider,Claudio

AU - Schulze-Tanzil,Gundula G.

AU - Schwegmann,Anita

AU - Sheng,Guojun

AU - Shin,Jay W.

AU - Sugiyama,Daisuke

AU - Sugiyama,Takaaki

AU - Summers,Kim M.

AU - Takahashi,Naoko

AU - Takai,Jun

AU - Tanaka,Hiroshi

AU - Tatsukawa,Hideki

AU - Tomoiu,Andru

AU - Toyoda,Hiroo

AU - Wetering,Marcvande

AU - Berg,Linda M.Van Den

AU - Verardo,Roberto

AU - Vijayan,DIpti

AU - Wells,Christine A.

AU - Winteringham,Louise N.

AU - Wolvetang,Ernst

AU - Yamaguchi,Yoko

AU - Yamamoto,Masayuki

AU - Yanagi-Mizuochi,Chiyo

AU - Yoneda,Misako

AU - Yonekura,Yohei

AU - Zhang,Peter G.

AU - Zucchelli,Silvia

AU - Abugessaisa,Imad

AU - Arner,Erik

AU - Harshbarger,Jayson

AU - Kondo,Atsushi

AU - Lassmann,Timo

AU - Lizio,Marina

AU - Sahin,Serkan

AU - Sengstag,Thierry

AU - Severin,Jessica

AU - Shimoji,Hisashi

AU - Suzuki,Masanori

AU - Suzuki,Harukazu

AU - Kawai,Jun

AU - Kondo,Naoto

AU - Itoh,Masayoshi

AU - Daub,Carsten O.

AU - Kasukawa,Takeya

AU - Kawaji,Hideya

AU - Carninci,Piero

AU - Forrest,Alistair R.R.

AU - Hayashizaki,Yoshihide

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.

U2 - 10.1038/sdata.2017.112

DO - 10.1038/sdata.2017.112

M3 - Article

VL - 4

JO - Scientific Data

T2 - Scientific Data

JF - Scientific Data

SN - 2052-4463

M1 - 170112

ER -

Noguchi S, Arakawa T, Fukuda S, Furuno M, Hasegawa A, Hori F et al. FANTOM5 CAGE profiles of human and mouse samples. Scientific Data. 2017 Aug 29;4. 170112. Available from, DOI: 10.1038/sdata.2017.112