Data Descriptor : FANTOM5 CAGE profiles of human and mouse samples

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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 , R , 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 , R A , Babina , M , Baillie , J K , Barnett , T C , Beckhouse , A G , Blumenthal , A , Bodega , B , Bonetti , A , Briggs , J , Brombacher , F , Carlisle , A J , Clevers , H C , Davis , C A , Detmar , M , Dohi , T , Edge , A S B , Edinger , M , Ehrlund , A , Ekwall , K , Endoh , M , Enomoto , H , Eslami , A , Fagiolini , M , Fairbairn , L , Farach-Carson , M C , Faulkner , G J , Ferrai , C , Fisher , M E , Forrester , L M , Fujita , R , Furusawa , J , Geijtenbeek , T B , Gingeras , T , Goldowitz , D , Guhl , S , Guler , R , Gustincich , S , Ha , T J , Hamaguchi , M , Hara , M , Hasegawa , Y , Herlyn , M , Heutink , P , Hitchens , K J , Hume , D A , Ikawa , T , Ishizu , Y , Kai , C , Kawamoto , H , Kawamura , Y I , Kempfle , J S , Kenna , T J , Kere , J , Khachigian , L M , Kitamura , T , Klein , S , Klinken , S P , Knox , A J , Kojima , S , Koseki , H , Koyasu , S , Lee , W , Lennartsson , A , Mackay-sim , A , Mejhert , N , Mizuno , Y , Morikawa , H , Morimoto , M , Moro , K , Morris , K J , Motohashi , H , Mummery , C L , 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 , D A , Passier , R , Patrikakis , M , Pombo , A , Pradhan-Bhatt , S , Qin , X-Y , Rehli , M , Rizzu , P , Roy , S , Sajantila , A , Sakaguchi , S , Sato , H , Satoh , H , Savvi , S , Saxena , A , Schmidl , C , Schneider , C , Schulze-Tanzil , G G , Schwegmann , A , Sheng , G , Shin , J W , Sugiyama , D , Sugiyama , T , Summers , K M , Takahashi , N , Takai , J , Tanaka , H , Tatsukawa , H , Tomoiu , A , Toyoda , H , van de Wetering , M , van den Berg , L M , Verardo , R , Vijayan , D , Wells , C A , Winteringham , L N , Wolvetang , E , Yamaguchi , Y , Yamamoto , M , Yanagi-Mizuochi , C , Yoneda , M , Yonekura , Y , Zhang , P G , 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 , C O , Kasukawa , T , Kawaji , H , Carninci , P , Forrest , A R R & Hayashizaki , Y 2017 , ' Data Descriptor : FANTOM5 CAGE profiles of human and mouse samples ' , Scientific data , vol. 4 , 170112 . https://doi.org/10.1038/sdata.2017.112

Title: Data Descriptor : FANTOM5 CAGE profiles of human and mouse samples
Author: 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
Contributor: University of Helsinki, Karolinska Institutet
University of Helsinki, Medicum
Date: 2017-08-29
Language: eng
Number of pages: 10
Belongs to series: Scientific data
ISSN: 2052-4463
URI: http://hdl.handle.net/10138/224407
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.
Subject: UCSC GENOME BROWSER
MAMMALIAN-CELLS
GENE-EXPRESSION
IN-VITRO
TRANSCRIPTION
ATLAS
VISUALIZATION
ENHANCERS
UPDATE
GROWTH
3111 Biomedicine
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