抄録
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.
| 本文言語 | English |
|---|---|
| 論文番号 | 170112 |
| ジャーナル | Scientific data |
| 巻 | 4 |
| DOI | |
| 出版ステータス | Published - 29-08-2017 |
| 外部発表 | はい |
All Science Journal Classification (ASJC) codes
- 統計学および確率
- 情報システム
- 教育
- コンピュータ サイエンスの応用
- 統計学、確率および不確実性
- 図書館情報学
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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; 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.研究成果: Article › 査読
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.
UR - http://www.scopus.com/inward/record.url?scp=85028461506&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85028461506&partnerID=8YFLogxK
U2 - 10.1038/sdata.2017.112
DO - 10.1038/sdata.2017.112
M3 - Article
C2 - 28850106
AN - SCOPUS:85028461506
VL - 4
JO - Scientific data
JF - Scientific data
SN - 2052-4463
M1 - 170112
ER -