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FANTOM5 CAGE profiles of human and mouse samples

Article scientifique 2017 Anglais

Résumé

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.

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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., Babina, M., Baillie, J., Barnett, T., Beckhouse, A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Carlisle, A., Clevers, H., Davis, C., Detmar, M., Dohi, T., Edge, A., Edinger, M., Ehrlund, A., Ekwall, K., Endoh, M., Enomoto, H., Eslami, A., Fagiolini, M., Fairbairn, L., Farach‐Carson, M., Faulkner, G., Ferrai, C., Fisher, M., Forrester, L., Fujita, R., Furusawa, J., Geijtenbeek, T., Gingeras, T., Goldowitz, D., Guhl, S., Guler, R., Gustincich, S., Ha, T., Hamaguchi, M., Hara, M., Hasegawa, Y., Herlyn, M., Heutink, P., Hitchens, K., Hume, D., Ikawa, T., Ishizu, Y., Kai, C., Kawamoto, H., Kawamura, Y., Kempfle, J., Kenna, T., Kere, J., Khachigian, L., Kitamura, T., Klein, S., Klinken, S., Knox, A., 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., Motohashi, H. (2017). FANTOM5 CAGE profiles of human and mouse samples. https://doi.org/10.1038/sdata.2017.112

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Auteur(s)

Shuhei Noguchi Takahiro Arakawa Shiro Fukuda Masaaki Furuno Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Kaoru Kaida Ai Kaiho Mutsumi Kanamori-Katayama Tsugumi Kawashima Miki Kojima Atsutaka Kubosaki Ri-ichiroh Manabe Mitsuyoshi Murata Sayaka Nagao-Sato Kenichi Nakazato Noriko Ninomiya Hiromi Nishiyori-Sueki Shohei Noma Eri Saijyo Akiko Saka Mizuho Sakai Christophe Simon Naoko Suzuki Michihira Tagami Shoko Watanabe Shigehiro Yoshida Peter Arner Richard A Axton Magda Babina J. Kenneth Baillie Timothy C. Barnett Anthony G Beckhouse Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher Ailsa J Carlisle Hans Clevers Carrie Davis Michael Detmar Taeko Dohi Albert S.B. Edge Matthias Edinger Anna Ehrlund Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Mary C. Farach‐Carson Geoffrey J. Faulkner Carmelo Ferrai Malcolm E Fisher Lesley M. Forrester Rie Fujita Jun-ichi Furusawa Teunis B. H. Geijtenbeek T Gingeras Dan Goldowitz Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Yuki Hasegawa Meenhard Herlyn Peter Heutink Kelly J Hitchens David Hume Tomokatsu Ikawa Yuri Ishizu Chieko Kai Hiroshi Kawamoto Yuki I. Kawamura Judith S. Kempfle Tony Kenna Juha Kere Levon M. Khachigian Toshio Kitamura Sarah Klein S. Peter Klinken Alan J. Knox Soichi Kojima Haruhiko Koseki Shigeo Koyasu Weon-Ju Lee Andreas Lennartsson Alan Mackay‐Sim Niklas Mejhert Yosuke Mizuno Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Kelly J Morris Hozumi Motohashi

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