Type
ArticleAuthors
Noguchi, ShuheiArakawa, 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
KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionBioscience Program
KAUST Environmental Epigenetics Research Program (KEEP)
Date
2017-08-29Online Publication Date
2017-08-29Print Publication Date
2017-12Permanent link to this record
http://hdl.handle.net/10754/625836
Metadata
Show full item recordAbstract
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.Citation
Noguchi S, Arakawa T, Fukuda S, Furuno M, Hasegawa A, et al. (2017) FANTOM5 CAGE profiles of human and mouse samples. Scientific Data 4: 170112. Available: http://dx.doi.org/10.1038/sdata.2017.112.Sponsors
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).Publisher
Springer NatureJournal
Scientific DataPubMed ID
28850106Additional Links
https://www.nature.com/articles/sdata2017112https://www.nature.com/articles/sdata2017112
Relations
Is Supplemented By:- [Dataset]
Clevers, H., Edge, A., Wetering, M. V. D., Detmar, M., Koseki, H., Edinger, M., Ekwall, K., Hume, D. A., Axton, R. A., Hara, M., Kitamura, T., Hasegawa, Y., Takahashi, N., Carninci, P., Wolvetang, E. J., Ovchinnikov, D., Davis, C., Hideya Kawaji, Gingeras, T., … Morikawa, H. (2017). FANTOM5 CAGE profiles of human and mouse samples. Figshare. https://doi.org/10.6084/M9.FIGSHARE.C.3728767.V1. DOI: 10.6084/m9.figshare.c.3728767.v1 Handle: 10754/664213 - [Software]
Title: hkawaji/dpi1: Decomposition-based peak identification, which find peaks across a large number of TSS (transcription starting site) profiles. Publication Date: 2013-12-25. github: hkawaji/dpi1 Handle: 10754/667011
ae974a485f413a2113503eed53cd6c53
10.1038/sdata.2017.112
Scopus Count
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