FANTOM5 CAGE profiles of human and mouse samples
Authors: 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 , Baillie J. Kenneth , 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 Albert S.B. , 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 , Klinken S. Peter , 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 , van de Wetering Marc , van den Berg Linda M. , 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 
Published: August 2017

AbstractIn 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.