Cited by 310Genomics and Chromatin DynamicsGenomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics
FANTOM5 CAGE profiles of human and mouse samples
Open accessNoguchi, Shuhei, Arakawa, Takahiro, Fukuda, Shiro, Furuno, Masaaki, Hasegawa, Akira, Hori, Fumi, Ishikawa-Kato, Sachi, Kaida, Kaoru +170 more·2017·Scientific Data
DOI 10.1038/sdata.2017.112PMC PMC5574368
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.
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CAGE assays help the model relate TSS usage and strength to RNA-seq coverage between multiple alternative TSSs.
“which we reasoned would help the model relate TSS usage and strength to RNA-seq coverage between multiple (alternative) TSSs97,98”
From Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation (2025) · cites this paper as [97]
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References 40 · Cited by 310
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- Authors
- 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.-I., 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.-I., 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.
- Affiliations
- RIKEN (JP)
- Karolinska University Hospital (SE)
- University of Edinburgh (GB)
- Charité – Universitätsmedizin Berlin (DE)
- Roslin Institute (GB)
- The University of Queensland (AU)
- Bio-Rad (United States) (US)
- Fondazione Santa Lucia (IT)
- South African Medical Research Council (ZA)
- Royal Netherlands Academy of Arts and Sciences (NL)
- Cold Spring Harbor Laboratory (US)
- ETH Zurich (CH)
- National Center for Global Health and Medicine (JP)
- Harvard University (US)
- University Hospital Regensburg (DE)
- Karolinska Institutet (SE)
- RIKEN Center for Integrative Medical Sciences (JP)
- Tokyo Medical and Dental University (JP)
- Mater Research (AU)
- Max Delbrück Center (DE)
- Tohoku University (JP)
- Amsterdam UMC Location University of Amsterdam (NL)
- Scuola Internazionale Superiore di Studi Avanzati (IT)
- University of British Columbia (CA)
- Immunology Frontier Research Center, The University of Osaka (JP)
- The Wistar Institute (US)
- German Center for Neurodegenerative Diseases (DE)
- Institute of Medical Science, The University of Tokyo (JP)
- Translational Research Institute (AU)
- King's College London (GB)
- UNSW Sydney (AU)
- Harry Perkins Institute of Medical Research (AU)
- University of Nottingham (GB)
- Saitama Medical University (JP)
- Leiden University Medical Center (NL)
- RIKEN BioResource Research Center (JP)
- Tokyo University of Pharmacy and Life Sciences (JP)
- Ohu University (JP)
- University of Delaware (US)
- University of Helsinki (FI)
- Consorzio Interuniversitario per le Biotecnologie (IT)
- Stiftung Charité (DE)
- International Research Center for Medical Sciences, Kumamoto University (JP)
- Kyushu University (JP)
- Nagoya University (JP)
- QIMR Berghofer Medical Research Institute (AU)
- The University of Melbourne (AU)
- Nihon University (JP)
- Kyushu University Hospital (JP)
- The Kids Research Institute Australia (AU)
- Corresponding author
- Kawaji, Hideya
- ORCID
- Arakawa, Takahiro
- Fukuda, Shiro
- Furuno, Masaaki
- Hasegawa, Akira
- Kawashima, Tsugumi
- Murata, Mitsuyoshi
- Nakazato, Kenichi
- Nishiyori-Sueki, Hiromi
- Noma, Shohei
- Tagami, Michihira
- Watanabe, Shoko
- Yoshida, Shigehiro
- Arner, Peter
- Babina, Magda
- Baillie, J. Kenneth
- Barnett, Timothy C.
- Beckhouse, Anthony G.
- Blumenthal, Antje
- Bodega, Beatrice
- Briggs, James
- Brombacher, Frank
- Clevers, Hans C.
- Detmar, Michael
- Dohi, Taeko
- Edge, Albert S.B.
- Edinger, Matthias
- Ekwall, Karl
- Endoh, Mitsuhiro
- Enomoto, Hideki
- Fagiolini, Michela
- Farach-Carson, Mary C.
- Faulkner, Geoffrey J.
- Ferrai, Carmelo
- Fisher, Malcolm E.
- Forrester, Lesley M.
- Geijtenbeek, Teunis B.
- Gingeras, Thomas
- Guhl, Sven
- Guler, Reto
- Gustincich, Stefano
- Hamaguchi, Masahide
- 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
- Knox, Alan J.
- Kojima, Soichi
- Koseki, Haruhiko
- Koyasu, Shigeo
- Lennartsson, Andreas
- Mejhert, Niklas
- Mizuno, Yosuke
- Morikawa, Hiromasa
- Morimoto, Mitsuru
- Moro, Kazuyo
- Motohashi, Hozumi
- Mummery, Christine L.
- Nakachi, Yutaka
- Nakahara, Fumio
- Nakamura, Yukio
- Ogishima, Soichi
- Ohkura, Naganari
- Ohno, Hiroshi
- Ohshima, Mitsuhiro
- Okazaki, Yasushi
- Orlando, Valerio
- Ovchinnikov, Dmitry A.
- Passier, Robert
- Pombo, Ana
- Pradhan-Bhatt, Swati
- Qin, Xian-Yang
- Rehli, Michael
- Rizzu, Patrizia
- Roy, Sugata
- Sajantila, Antti
- Sakaguchi, Shimon
- Sato, Hiroki
- Satoh, Hironori
- Saxena, Alka
- Schmidl, Christian
- Schulze-Tanzil, Gundula G.
- Sheng, Guojun
- Shin, Jay W.
- Sugiyama, Daisuke
- Summers, Kim M.
- Takahashi, Naoko
- Tanaka, Hiroshi
- Tatsukawa, Hideki
- Tomoiu, Andru
- Vijayan, Dipti
- Wells, Christine A.
- Winteringham, Louise N.
- Wolvetang, Ernst
- Yamamoto, Masayuki
- Zhang, Peter G.
- Zucchelli, Silvia
- Abugessaisa, Imad
- Harshbarger, Jayson
- Kondo, Atsushi
- Lassmann, Timo
- Lizio, Marina
- Sengstag, Thierry
- Severin, Jessica
- Suzuki, Harukazu
- Kawai, Jun
- Itoh, Masayoshi
- Daub, Carsten O.
- Kasukawa, Takeya
- Kawaji, Hideya
- Carninci, Piero
- Forrest, Alistair R.R.
- Hayashizaki, Yoshihide
- Venue
- Scientific Data
- Published
- 2017-08-29
- Volume
- 4
- Issue
- 1
- Pages
- 170112-170112
- ISSN
- 2052-4463 (ISSN-L)
- PMC
- PMC5574368
- OpenAlex
- W2750304043
- Cited by
- 310
- References
- 40
- Citations by year
- 2026: 27 · 2025: 35 · 2024: 53 · 2023: 48 · 2022: 37 · 2021: 47 · 2020: 33 · 2019: 18 · 2018: 8 · 2017: 3 · 2013: 1
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- data paper
- Language
- en
- Open access
- gold
- doi.org
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- ETH Zürich Research Collection (cc-by)
- Funders
- Melanoma Research Alliance
- Child and Family Research Institute
- Wellcome Trust (103258/Z/13/Z)
- University of Texas Health Science Center at Houston
- South African Medical Research Council
- International Centre for Genetic Engineering and Biotechnology
- Ministry of Education, Culture, Sports, Science and Technology (10117)
- University of Queensland (QLD 4072)
- Universiteit van Amsterdam
- Eidgenössische Technische Hochschule Zürich
- Karolinska Institutet
- Deutsches Zentrum für Neurodegenerative Erkrankungen
- Universitätsklinikum Regensburg
- University of Cape Town
- Tokyo Medical and Dental University
- National Institutes of Health (5p30ca045508-35)
- Medical Research Council
- Biotechnology and Biological Sciences Research Council (BBS/E/D/20211552, BB/H008098/1, BBS/E/D/20211550, BBS/E/D/20211551, BBS/E/D/20241863, BBS/E/D/30002275, BBS/E/D/10002070, BBS/E/D/20221657)
- Japan Society for the Promotion of Science (16H02587, 15H04744, 17H04214, 16K07372, 15K08539, 16K00385)
- RIKEN
- Diamantina Institute, University of Queensland
- National Cancer Institute (P20CA192996, P30-CA045508, P30CA010815)
- National Institute on Deafness and Other Communication Disorders (R01DC014089)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD090255)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- transcription initiation, CAGE, FANTOM5, promoter mapping, transcription start sites, single-molecule sequencing, human genome, mouse genome, cell activation, development (biology), tissue-specific gene expression, transcriptional regulation
- MeSH terms
- Animals, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Species Specificity, Genome, Gene Expression Profiling, Mice
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