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1. Impacts of Ni-Loading Method on the Structure and the Catalytic Activity of NiO/SiO2-Al2O3 for Ethylene Oligomerization

Author

Katsuya Shimura, Shigehiro Yoshida, Hiroshi Oikawa, and Tadahiro Fujitani

Subjects
ethylene oligomerization, NiO/SiO2-Al2O3 catalyst, ion-exchange, impregnation, homogeneous precipitation, Chemical technology, TP1-1185, Chemistry, QD1-999
Abstract

To clarify the Ni species of NiO/SiO2-Al2O3 catalysts that are active for ethylene oligomerization, 18 types of NiO/SiO2-Al2O3 were prepared using three Ni-loading methods (i.e., ion-exchange, impregnation, and homogeneous precipitation), with different Ni-loadings (1–20 wt%), and examined with respect to their structure and catalytic activity for ethylene oligomerization. Characterized by N2 adsorption, powder XRD, FE-SEM, H2-TPR, NH3-TPD, and C2H4-TPD showed that Ni species in the catalysts prepared by ion-exchange were mainly ion-exchanged Ni cations. In contrast, Ni species in the catalysts prepared by impregnation were a mixture of ion-exchanged Ni cations and NiO particles, and those in the catalysts prepared by homogeneous precipitation were all NiSiO3 particles. Catalytic-reaction tests at 300 °C and 0.1 MPa revealed the following: the ion-exchanged Ni cations showed the highest C2H4 conversion rate; the NiSiO3 particles showed a moderate reaction rate; and the NiO particles were not active for ethylene oligomerization. We concluded that the high catalytic activity of the ion-exchanged Ni cations was a result of their high dispersion and medium-strength acidity, which together promoted the adsorption and activation of ethylene on, and the desorption of oligomerization products from, the catalyst.

Published
2023
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3. A promoter-level mammalian expression atlas.

Author

The Fantom Consortium, RIKEN PMII, RIKEN CLST (DGT), Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. M. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, Takahiro Arakawa, John A. C. Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans Clevers, Emiliano Dalla, Carrie A. Davis, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S. B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas R. Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F. J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-Sim, Ri-ichiroh Manabe, Jessica Cara Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison M. Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik van Nimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G. D. Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B. Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, Mizuho Sakai, Hiroki Sato, Hironori Sato, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C. 't Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson 0002, Hiroo Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Susan E. Zabierowski, Peter G. Zhang, Xiaobei Zhao, Silvia Zucchelli, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci, and Yoshihide Hayashizaki

Published
2014
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6. Surface Change of Liquid Ga Electrode By Na Electrodeposition in NaTf2N-TEATf2N Ionic Liquid

Author

Takehiko Kumagai, Mikito Ueda, Hisayoshi Matsushima, and Shigehiro Yoshida

Subjects
chemistry.chemical_compound, Materials science, chemistry, Chemical engineering, Ionic liquid, Surface change, Electrode
Abstract

A liquid metal electrode has interesting property such as phase change from a liquid to a solid depend on alloys composition. There are many reports of solid metal deposition on a liquid electrode, there are few papers of liquid metal deposition on a liquid electrode. In this study, Ga was used as the liquid electrode and Na electrodeposition was carried out in ionic liquid electrolyte at 160 oC. Since the melting point of Ga and Na are 29.8 and the 97.8 oC, at the moment when Na is electrodeposited, the liquid Na presents on the liquid Ga. In this experiment, we focused on the surface change of the Ga electrode before and after the electrodeposition of liquid Na. The experiment was conducted in a glove box under Ar atmosphere. NaTf2N (Sodium bis (trifluoromethanesulfonyl) imide) -TEATf2N (Tetraethylammonium bis (trifluoromethanesulfonyl) imide) mixed ionic liquid with molar ratio of 1 : 4 was used as an electrolyte at 160 oC. Liquid Ga or solid Ag plate was used as a working electrode and liquid Na was used as counter electrode and reference electrode. The voltammogram measurement was performed in the range from 2.5 V to -0.5 V (vs. Na/Na+) with sweep rate of 10 mV s-1. Constant current electrolysis was carried out at 5 mAcm-2 for 3 minutes. The liquid Ga electrode surface was taken by a digital camera. The time change of the open circuit potential of the Ga electrode after constant current electrolysis was measured by potentiostat. In voltammogram measurement, cathodic current on Ag working electrode flowed at lower than 0.0 V (vs. Na / Na +). In the liquid Ga electrode, cathodic current started at 0.6 V, then the cathodic current increased again at lower than about 0 V. The color of the liquid Ga surface changed slightly from bright metallic to black and gray. When the potential was reversed to anodic direction, the color of the Ga surface changed to gray, black and bright metallic. In liquid Ga electrode, start of cathodic current was more positive potential compared with solid Ag electrode. It is considered the cathodic current at range from 0.0 to 0.6 V may relate to formation of Na-Ga intermetallic compound. In constant current electrolysis, the potential change showed in two steps with similar the voltammogram measurement, color of the Ga surface changed to black in the first step and gray in the second step. In the open-circuit potential measurement, 3 potential plateaus of 1.9, 0.58, and 0.38 V (vs. Na / Na +) were observed. The potential plateau at 1.9 V corresponds to pure Ga, the potential plateaus 0.58 and 0.38 V may correspond to Na-Ga intermetallic compounds with different composition. It is known from the Na-Ga binary phase diagram that there are two intermetallic compounds, Ga4Na and Ga39Na22. In the surface color change of Ga electrode to black, it is considered that formation of Ga4Na on the surface because small amount of Na liquid was electrodeposited on the Ga electrode. Further, by depositing Na on the surface, Ga39Na22 may be formed on the surface, and even if more Na is deposited on Ga39Na22, the intermetallic compound does not change any more, and metal Na is deposited on the Ga39Na22. Therefore, the color of the electrode surface may have changed from black to gray.

Published
2020

7. FANTOM5 CAGE profiles of human and mouse samples

Author

Jun Kawai, Anthony G Beckhouse, Dipti Vijayan, Michael Rehli, Toshiyuki Nakamura, Yuki Hasegawa, Timothy C. Barnett, Hisashi Shimoji, Erik Arner, Masayoshi Itoh, Masahide Hamaguchi, Sarah Klein, Reto Guler, Patrizia Rizzu, Atsutaka Kubosaki, Soichi Kojima, Timo Lassmann, Kelly J. Morris, Mutsumi Kanamori-Katayama, Ri Ichiroh Manabe, Hiromasa Morikawa, Kelly J Hitchens, Fumi Hori, Linda M. van den Berg, Yasushi Okazaki, Andru Tomoiu, Antti Sajantila, Akiko Saka, Thierry Sengstag, Alessandro Bonetti, Haruhiko Koseki, Matthias Edinger, Mitsuhiro Ohshima, Carsten O. Daub, Jayson Harshbarger, Sachi Ishikawa-Kato, Tsugumi Kawashima, Christine L. Mummery, Niklas Mejhert, Jun Takai, Dan Goldowitz, Naoko Suzuki, Guojun Sheng, David A. Hume, Hiroshi Kawamoto, Ai Kaiho, Jun Ichi Furusawa, Ailsa J Carlisle, Tomokatsu Ikawa, Shiro Fukuda, Peter G. Zhang, Akira Hasegawa, James Briggs, Toshio Kitamura, Alistair R. R. Forrest, Takahiro Arakawa, Marcvande Wetering, Shohei Noma, Fumio Nakahara, Jessica Severin, Sven Guhl, Atsushi Kondo, Mary C. Farach-Carson, Hans Clevers, Afsaneh Eslami, Christian Schmidl, Peter Heutink, Hideki Tatsukawa, Anita Schwegmann, Noriko Ninomiya, Antje Blumenthal, Yoshihide Hayashizaki, Suzana Savvi, Thomas J. Ha, Claudio Schneider, Daisuke Sugiyama, Hironori Satoh, Mitsuru Morimoto, Hiroki Sato, Yosuke Mizuno, Meenhard Herlyn, Hozumi Motohashi, Shigehiro Yoshida, Hiroo Toyoda, Christophe Simon, Piero Carninci, Tadasuke Nozaki, Hideya Kawaji, Louise N. Winteringham, Swati Pradhan-Bhatt, Imad Abugessaisa, Michihira Tagami, Tony J. Kenna, Yoko Yamaguchi, Geoffrey J. Faulkner, Alka Saxena, Naoto Kondo, Dmitry A. Ovchinnikov, Rie Fujita, Ernst J. Wolvetang, Michael Detmar, Miki Kojima, Peter Arner, Mitsuko Hara, Stefano Gustincich, Carrie A. Davis, Judith S. Kempfle, Margaret Patrikakis, Alan Mackay-Sim, Carmelo Ferrai, Yutaka Nakachi, Juha Kere, Mitsuyoshi Murata, Shimon Sakaguchi, Soichi Ogishima, Silvia Zucchelli, Andreas Lennartsson, Thomas R. Gingeras, Masanori Suzuki, Beatrice Bodega, Sugata Roy, Sayaka Nagao-Sato, Mitsuhiro Endoh, Anna Ehrlund, J Kenneth Baillie, Mizuho Sakai, Michela Fagiolini, Taeko Dohi, Christine A. Wells, Frank Brombacher, Masayuki Yamamoto, Robert Passier, Lynsey Fairbairn, Teunis B. H. Geijtenbeek, Shigeo Koyasu, Hiromi Nishiyori-Sueki, Yuri Ishizu, Yuki I. Kawamura, Chiyo Yanagi-Mizuochi, Roberto Verardo, Misako Yoneda, Mariko Okada-Hatakeyama, Kaoru Kaida, Ana Pombo, Gundula Schulze-Tanzil, Lesley M. Forrester, Kim M. Summers, Harukazu Suzuki, Naganari Ohkura, Weon Ju Lee, Hiroshi Tanaka, Alan J. Knox, Karl Ekwall, Yukio Nakamura, Serkan Sahin, Shuhei Noguchi, Hiroshi Ohno, Yohei Yonekura, Richard A Axton, Marina Lizio, S. Peter Klinken, Malcolm E. Fisher, Shoko Watanabe, Magda Babina, Xian-Yang Qin, Takaaki Sugiyama, B. Albert S. Edge, Eri Saijyo, Valerio Orlando, Takeya Kasukawa, Kazuyo Moro, Kenichi Nakazato, Naoko Takahashi, Levon M. Khachigian, Chieko Kai, Masaaki Furuno, Jay W. Shin, Hideki Enomoto, Hubrecht Institute for Developmental Biology and Stem Cell Research, AII - Infectious diseases, Infectious diseases, and AII - Amsterdam institute for Infection and Immunity

Subjects
0301 basic medicine, 500 Naturwissenschaften und Mathematik::570 Biowissenschaften, Biologie, Data Descriptor, Molecular biology, 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit, Genome, Mice, 0302 clinical medicine, Transcription (biology), Promoter Regions, Genetic, Non-U.S. Gov't, Regulation of gene expression, Research Support, Non-U.S. Gov't, Statistics, Computer Science Applications1707 Computer Vision and Pattern Recognition, Computer Science Applications, Library and Information Sciences, Information Systems, Statistics, Probability and Uncertainty, Statistics and Probability, ddc:500, Cell activation, Systems biology, Cell biology, Computational biology, Biology, Research Support, Education, 03 medical and health sciences, Species Specificity, Developmental biology, Journal Article, Animals, Humans, Enhancer, Gene Expression Profiling, Promoter, Cap analysis gene expression, Computational biology and bioinformatics, Gene expression profiling, 030104 developmental biology, Gene Expression Regulation, Cardiovascular and Metabolic Diseases, Probability and Uncertainty, 030217 neurology & neurosurgery
Abstract

Scientific Data, 4, ISSN:2052-4463

Published
2017
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8. A STUDY ON THE RADIOACTIVE MATERIAL IN THE FRONT SEA AREA OF THE MAMA-RIVER MOUTH

Author

Shigehiro Yoshida, Toshimasa Kawanishi, Fumikazu Otsuka, Sousuke Nakamoto, and Koichi Masuda

Subjects
060201 languages & linguistics, Hydrology, geography, geography.geographical_feature_category, 0602 languages and literature, 0202 electrical engineering, electronic engineering, information engineering, River mouth, Radioactive waste, Environmental science, 020201 artificial intelligence & image processing, 06 humanities and the arts, 02 engineering and technology, Front (military)
Published
2017

9. 2-D Interpolation of Thrust and Lift Forces in Controlled-PM LSM, Based on Analytical Formulas and FEA

Author

Shigehiro Yoshida, Kinjiro Yoshida, and Hiroshi Takami

Subjects
Engineering, business.industry, CPU time, Thrust, Structural engineering, Linear motor, Industrial and Manufacturing Engineering, Finite element method, Lift (force), Vehicle dynamics, Maglev, Central processing unit, Electrical and Electronic Engineering, business
Abstract

Thrust and lift forces in controlled-PM linear synchronous motor (LSM) can be analyzed exactly by using FEM, taking into account the effect of slots. Especially in the controlled-PM LSM Maglev vehicle, large slots are adopted to manufacture quite easily its long-stator guideway. But a vast CPU time is required for FEM simulations of the vehicle dynamics. A method for calculating the thrust and lift forces is presented here which can keep high accuracy of finite element analysis (FEA) and reduce extremely the CPU time. Two-dimensional interpolation of this method is derived on the basis of analytical formulas and FEA of the machine. It is shown from numerical example of 1/2-scale controlled-PM LSM Maglev vehicle that the method proposed here enables us to calculate the thrust and lift forces with the same accuracy as FEM.

Published
1997

10. Thermal stabilization of lipase by sol-gel entrapment in organically modified silicates formed on kieselguhr

Author

Koei Kawakami and Shigehiro Yoshida

Subjects
Silanes, Immobilized enzyme, biology, Chemistry, Methyltrimethoxysilane, Triacylglycerol lipase, Applied Microbiology and Biotechnology, Catalysis, chemistry.chemical_compound, Chemical engineering, biology.protein, Organic chemistry, Thermal stability, Lipase, Biotechnology, Sol-gel
Abstract

The catalytic activity and thermal stability of lipase entrapped in organically modified silicates by the sol-gel method have been studied in ester synthesis in organic solvents. When methyltrimethoxysilane (MTrMOS) was used as the organic silane precursor which was mixed with tetramethoxysilane (TMOS) at a molar ratio of 3 : 1, the entrapped lipase exhibited a higher esterification activity than the lipase deposited on Celite 545 at temperatures as high as 65°C. This esterification activity was further enhanced by forming the lipase-entrapping gel on the surface of Celite 545. Thermal stabilization of lipase by entrapment in hybrid gels seems to be closely related to the mechanism of the sol-gel transition accompanied by microscopic phase separation. As a result of screening of different organic silanes, and of optimization of the preparation conditions, the hybrid gel-entrapped lipases on Celite 545 derived from an equimolar mixture of either propyltrimethoxysilane or trimethylmethoxysilane and TMOS were found to be the most thermostable, retaining their full activities up to 75°C, and 100 to 200 times higher activity at 95°C compared to the lipase deposited on the same support.

Published
1996

11. Sol-gel entrapment of lipase using a mixture of tetramethoxysilane and methyltrimethoxysilane as the alkoxide precursor: Esterification activity in organic media

Author

Shigehiro Yoshida and Koei Kawakami

Subjects
biology, Immobilized enzyme, Methyltrimethoxysilane, Triacylglycerol lipase, Applied Microbiology and Biotechnology, Biochemistry, Silicon alkoxide, chemistry.chemical_compound, Entrapment, chemistry, Alkoxide, biology.protein, Organic chemistry, Lipase, Sol-gel
Abstract

The sol-gel method, using a mixture of tetramethoxysilane (TMOS) and methyltrimethoxysilane (MTrMOS) as the silicon alkoxide precursor, has been applied to entrapment of lipase catalyzing esterification reactions in organic media. Increasing molar ratio of MTrMOS to TMOS led to formation of opaque and non-shrinkable gels and resulted in an increase in the esterification activity of lipase. The hybrid gel-entrapped lipase based on [MTrMOS]/[TMOS] ratio of 4 exhibited almost equal activity with those of the deposited lipase on different supports at 35°C, and retained ca. ten times higher activity than the deposited counterparts at 65 °C.

Published
1995

12. Entrapment of lipase in silica glass by the sol-gel method and its esterification activity in organic media

Author

Shigehiro Yoshida and Koei Kawakami

Subjects
Chromatography, Immobilized enzyme, biology, Chemistry, technology, industry, and agriculture, Triacylglycerol lipase, Applied Microbiology and Biotechnology, Biochemistry, Butyric acid, Hexane, chemistry.chemical_compound, Entrapment, biology.protein, Lipase, Shrinkage, Sol-gel
Abstract

Silica glass-entrapped lipase was prepared by the sol-gel method using tetramethoxysilane, and its esterification activity in n-hexane was examined for isoamylbutyrate formation. The hydrogel preparation containing a large amount of water exhibited enough activity. Although the activity of xerogel-entrapped lipase drastically decreased probably due to shrinkage of the gel matrix, the lyophilized gel retained much higher activity than the air-dried gel.

Published
1994

13. A promoter-level mammalian expression atlas

Author

Frank Brombacher, Wyeth W. Wasserman, Hiromasa Morikawa, Fumi Hori, Sayaka Nagao-Sato, Artem S. Kasianov, Mitsuhiro Endoh, Ilka Hoof, Hans Clevers, Hideki Tatsukawa, Anita Schwegmann, Kang Li, David A. de Lima Morais, Yoshihide Hayashizaki, Morana Vitezic, Judith A. Blake, Leonard Lipovich, Hozumi Motohashi, Timothy Ravasi, Meenhard Herlyn, Shuji Kawaguchi, Antti Sajantila, Haruhiko Koseki, Lukasz Huminiecki, Tsugumi Kawashima, Carrie A. Davis, Mamoon Rashid, Winston Hide, Alka Saxena, Mizuho Sakai, Carsten O. Daub, Kim M. Summers, Yuki Hasegawa, Hisashi Shimoji, Margaret Patrikakis, Efthymios Motakis, Morten Beck Rye, Dan Goldowitz, Masaaki Furuno, Lynsey Fairbairn, Alan Mackay-Sim, Andreas Lennartsson, John A.C. Archer, Mitsuru Morimoto, Harukazu Suzuki, Silvia Zucchelli, Weon Ju Lee, Hiroki Sato, Alan J. Knox, Margherita Francescatto, Xiaobei Zhao, Jay W. Shin, Thomas R. Gingeras, Soichi Ogishima, Jayson Harshbarger, Mark Thompson, Beatrice Bodega, Marco Chierici, Shintaro Katayama, Albin Sandelin, Sarah Rennie, Silvano Piazza, Tomokatsu Ikawa, Matthias Harbers, Magda Babina, Peter G. Zhang, Gabriel M. Altschule, Lenhard Vladimir B. Bajic, Andrew P. Gibson, Malcolm E. Fisher, Karl Ekwall, Yukio Nakamura, Arnab Pain, Michiel J. L. de Hoon, Toshio Kitamura, Anthony G Beckhouse, Ai Kaiho, Julian Gough, James Briggs, Jordan A. Ramilowski, Miki Kojima, Alistair R. R. Forrest, Erik Anthony Schultes, Jessica C. Mar, Dipti Vijayan, Peter Arner, S. Peter Klinken, Michael Rehli, Kazuhiro Kajiyama, Christophe Simon, Piero Carninci, Marco Roncador, Shigeo Koyasu, Mary C. Farach-Carson, Shigehiro Yoshida, Swati Pradhan-Bhatt, Zuotian Tatum, Masanori Suzuki, Mette C. Jørgensen, Benoit Marchand, Misako Yoneda, James Prendergast, Noriko Ninomiya, Tom C. Freeman, Yulia A. Medvedeva, Niklas Mejhert, Jun Takai, Alexander D. Diehl, Akiko Saka, Marc van de Wetering, Takehiro Hashimoto, Naoto Kondo, Martin S. Taylor, Albert S.B. Edge, Mutsumi Kanamori-Katayama, Colin A. Semple, Alexander V. Favorov, Giuseppe Jurman, Toshiyuki Nakamura, Thomas J. Ha, Yuri Ishizu, Shannan J. Ho Sui, David A. Hume, Owen J. L. Rackham, Michela Fagiolini, Daisuke Sugiyama, Helena Persson, Hironori Satoh, Robert Young, Emily J. Wood, Akira Hasegawa, Yosuke Mizuno, Juha Kere, Hiroshi Tanaka, Michihira Tagami, A. Maxwell Burroughs, Sugata Roy, Sachi Kato, Taeko Dohi, Hai Fang, Chieko Kai, Fumio Nakahara, Christian Schmidl, Hiromi Nishiyori, Thierry Sengstag, Sven Guhl, Kei Iida, Antje Blumenthal, Boris Lenhard, Sarah Krampitz, Peter A C 't Hoen, Piotr J. Balwierz, Masayuki Yamamoto, Eri Saijyo, Suzana Savvi, Intikhab Alam Altschuler, Marina Lizio, Alison M. Meynert, Kazuyo Moro, Kenichi Nakazato, Sebastian Schmeier, Carlo Vittorio Cannistraci, Yasushi Okazaki, Yishai Shimoni, Kelly J Hitchens, Hideki Enomoto, Jeroen F. J. Laros, Naganari Ohkura, Ilya E. Vorontsov, Davide Albanese, Hiroshi Ohno, Yun Chen, Terrence F. Meehan, Mitsuhiro Ohshima, Mitsuko Hara, Emiliano Dalla, Roberto Verardo, Claudio Schneider, Takahiro Arakawa, Oliver Hofmann, Matthias Edinger, Mariko Okada-Hatakeyama, Susan E. Zabierowski, Shohei Noma, Yutaka Nakachi, Shoko Watanabe, Kaoru Kaida, Mitsuyoshi Murata, Takaaki Sugiyama, Hui Jia, Tetsuro Toyoda, Naoko Suzuki, Vsevolod J. Makeev, Naoko Takahashi Tagami, Hiroko Ohmiya, Christine L. Mummery, Emmanuel Dimont, Shiro Fukuda, Jun Kawai, Ivan V. Kulakovskiy, Anthony Mathelier, Nicolas Bertin, Hiroshi Kawamoto, Vanja Haberle, Robert Passier, Levon M. Khachigian, Yuki I. Kawamura, Jessica Severin, Valerio Orlando, Takeya Kasukawa, Teunis B. H. Geijtenbeek, Charles Plessy, Ernst J. Wolvetang, Stefano Gustincich, Shimon Sakaguchi, Erik van Nimwegen, Reto Guler, Martin C. Frith, Andrea Califano, Timo Lassmann, Peter Heutink, Boris R. Jankovic, Ri Ichiroh Manabe, Berit Lilje, Yari Ciani, Erik Arner, Rie Fujita, Robin Andersson, J Kenneth Baillie, Andrew T. Kwon, Atsutaka Kubosaki, Jun Ichi Furusawa, Soichi Kojima, Daniel Carbajo, Christine A. Wells, Tadasuke Nozaki, Rolf Swoboda, Hiroo Toyoda, Tony J. Kenna, Yoko Yamaguchi, Hideya Kawaji, Louise N. Winteringham, Cesare Furlanello, Michael Detmar, Judith S. Kempfle, Bogumil Kaczkowski, Gundula G. Schulze-Tanzil, Linda M. van den Berg, Alessandro Bonetti, Eivind Valen, Masayoshi Itoh, Yohei Yonekura, Guojun Sheng, Ulf Schaefer, Masahide Hamaguchi, Patrizia Rizzu, Anagha Joshi, Dmitry A. Ovchinnikov, Finn Drabløs, Christopher J. Mungall, Geoffrey J. Faulkner, Hubrecht Institute for Developmental Biology and Stem Cell Research, AII - Amsterdam institute for Infection and Immunity, Infectious diseases, Experimental Immunology, Human genetics, and NCA - Brain mechanisms in health and disease

Subjects
Transcription, Genetic, Cells, Messenger, Gene regulatory network, Mammalian promoter database, Biology, Article, Cell Line, Promoter Regions, Mice, Open Reading Frames, Essential, Atlases as Topic, Genetic, Animals, Cluster Analysis, Humans, Gene Regulatory Networks, RNA, Messenger, Promoter Regions, Genetic, Gene, Transcription factor, Cells, Cultured, Conserved Sequence, Genetics, Regulation of gene expression, Cultured, Multidisciplinary, Genes, Essential, Genome, Promoter, Molecular Sequence Annotation, Cap analysis gene expression, Genes, Gene Expression Regulation, Organ Specificity, Transcription Factors, Transcription Initiation Site, Transcriptome, RNA, Human genome, Transcription
Abstract

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

Published
2014

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