Helmholtz Gemeinschaft


FANTOM5 CAGE profiles of human and mouse samples

PDF (Article) - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
PDF (Supplementary Information) - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader

Item Type:Article
Title:FANTOM5 CAGE profiles of human and mouse samples
Creators Name:Noguchi, S. and Arakawa, T. and Fukuda, S. and Furuno, M. and Hasegawa, A. and Hori, F. and Ishikawa-Kato, S. and Kaida, K. and Kaiho, A. and Kanamori-Katayama, M. and Kawashima, T. and Kojima, M. and Kubosaki, A. and Manabe, R.I. and Murata, M. and Nagao-Sato, S. and Nakazato, K. and Ninomiya, N. and Nishiyori-Sueki, H. and Noma, S. and Saijyo, E. and Saka, A. and Sakai, M. and Simon, C. and Suzuki, N. and Tagami, M. and Watanabe, S. and Yoshida, S. and Arner, P. and Axton, R.A. and Babina, M. and Baillie, J.K. and Barnett, T.C. and Beckhouse, A.G. and Blumenthal, A. and Bodega, B. and Bonetti, A. and Briggs, J. and Brombacher, F. and Carlisle, A.J. and Clevers, H.C. and Davis, C.A. and Detmar, M. and Dohi, T. and Edge, A.S.B. and Edinger, M. and Ehrlund, A. and Ekwall, K. and Endoh, M. and Enomoto, H. and Eslami, A. and Fagiolini, M. and Fairbairn, L. and Farach-Carson, M.C. and Faulkner, G.J. and Ferrai, C. and Fisher, M.E. and Forrester, L.M. and Fujita, R. and Furusawa, J.I. and Geijtenbeek, T.B. and Gingeras, T. and Goldowitz, D. and Guhl, S. and Guler, R. and Gustincich, S. and Ha, T.J. and Hamaguchi, M. and Hara, M. and Hasegawa, Y. and Herlyn, M. and Heutink, P. and Hitchens, K.J. and Hume, D.A. and Ikawa, T. and Ishizu, Y. and Kai, C. and Kawamoto, H. and Kawamura, Y.I. and Kempfle, J.S. and Kenna, T.J. and Kere, J. and Khachigian, L.M. and Kitamura, T. and Klein, S. and Klinken, S.P. and Knox, A.J. and Kojima, S. and Koseki, H. and Koyasu, S. and Lee, W. and Lennartsson, A.s and Mackay-Sim, A. and Mejhert, N. and Mizuno, Y. and Morikawa, H. and Morimoto, M. and Moro, K. and Morris, K.J. and Motohashi, H. and Mummery, C.L. and Nakachi, Y. and Nakahara, F. and Nakamura, T. and Nakamura, Y. and Nozaki, T. and Ogishima, S. and Ohkura, N. and Ohno, H. and Ohshima, M. and Okada-Hatakeyama, M. and Okazaki, Y. and Orlando, V. and Ovchinnikov, D.A. and Passier, R. and Patrikakis, M. and Pombo, A. and Pradhan-Bhatt, S. and Qin, X.Y. and Rehli, M. and Rizzu, P. and Roy, S. and Sajantila, A. and Sakaguchi, S. and Sato, H. and Satoh, H. and Savvi, S. and Saxena, A. and Schmidl, C. and Schneider, C. and Schulze-Tanzil, G.G. and Schwegmann, A. and Sheng, G. and Shin, J.W. and Sugiyama, D. and Sugiyama, T. and Summers, K.M. and Takahashi, N. and Takai, J. and Tanaka, H. and Tatsukawa, H. and Tomoiu, A. and Toyoda, H. and van de Wetering, M. and van den Berg, L.M. and Verardo, R. and Vijayan, D. and Wells, C.A. and Winteringham, L.N. and Wolvetang, E. and Yamaguchi, Y. and Yamamoto, M. and Yanagi-Mizuochi, C. and Yoneda, M. and Yonekura, Y. and Zhang, P.G. and Zucchelli, S. and Abugessaisa, I. and Arner, E. and Harshbarger, J. and Kondo, A. and Lassmann, T. and Lizio, M. and Sahin, S. and Sengstag, T. and Severin, J. and Shimoji, H. and Suzuki, M. and Suzuki, H. and Kawai, J. and Kondo, N. and Itoh, M. and Daub, C.O. and Kasukawa, T. and Kawaji, H. and Carninci, P. and Forrest, A.R.R. and Hayashizaki, Y.
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.
Keywords:Gene Expression Profiling, Genome, Promoter Regions, Genetic, Species Specificity, Animals, Mice
Source:Scientific Data
Publisher:Nature Publishing Group
Page Range:170112
Date:29 August 2017
Official Publication:https://doi.org/10.1038/sdata.2017.112
PubMed:View item in PubMed

Repository Staff Only: item control page


Downloads per month over past year

Open Access
MDC Library