Abstract
| Original language | English (US) |
|---|---|
| Journal | Scientific data |
| Volume | 4 |
| Issue number | 1 |
| DOIs | |
| State | Published - Aug 29 2017 |
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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
AU - Kaida, Kaoru
AU - Kaiho, Ai
AU - Kanamori-Katayama, Mutsumi
AU - Kawashima, Tsugumi
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 - Baillie, J. Kenneth
AU - Mummery, Christine L.
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 - Nakachi, Yutaka
AU - Detmar, Michael
AU - Dohi, Taeko
AU - Edge, Albert S.B.
AU - Edinger, Matthias
AU - Ehrlund, Anna
AU - Ekwall, Karl
AU - Endoh, Mitsuhiro
AU - Enomoto, Hideki
AU - Eslami, Afsaneh
AU - Fagiolini, Michela
AU - Nakahara, Fumio
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 - Nakamura, Toshiyuki
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 - Nakamura, Yukio
AU - Hitchens, Kelly J.
AU - Hume, David A.
AU - Ikawa, Tomokatsu
AU - Orlando, Valerio
AU - Kai, Chieko
AU - Kawamoto, Hiroshi
AU - Kawamura, Yuki I.
AU - Kempfle, Judith S.
AU - Kenna, Tony J.
AU - Kere, Juha
AU - Nozaki, Tadasuke
AU - Khachigian, Levon M.
AU - Kitamura, Toshio
AU - Klein, Sarah
AU - Klinken, S. Peter
AU - Knox, Alan J.
AU - Kojima, Soichi
AU - Koseki, Haruhiko
AU - Koyasu, Shigeo
AU - Lee, Weonju
AU - Lennartsson, Andreas
AU - Ogishima, Soichi
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 - Ohkura, Naganari
AU - Ohno, Hiroshi
AU - Ohshima, Mitsuhiro
AU - Kojima, Miki
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 - Kubosaki, Atsutaka
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 - Manabe, Ri-ichiroh
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 - Murata, Mitsuyoshi
AU - Tatsukawa, Hideki
AU - Tomoiu, Andru
AU - Toyoda, Hiroo
AU - van de Wetering, Marc
AU - van den Berg, Linda M.
AU - Verardo, Roberto
AU - Vijayan, Dipti
AU - Wells, Christine A.
AU - Winteringham, Louise N.
AU - Wolvetang, Ernst
AU - Nagao-Sato, Sayaka
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 - Nakazato, Kenichi
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 - Ninomiya, Noriko
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
AU - Nishiyori-Sueki, Hiromi
AU - Noma, Shohei
AU - Saijyo, Eri
AU - Saka, Akiko
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 -