FANTOM5 CAGE profiles of human and mouse samples

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Noguchi, S (author)

FANTOM5 CAGE profiles of human and mouse samples

Article/chapterEnglish2017

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2017-08-29
Springer Science and Business Media LLC,2017

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LIBRIS-ID:oai:prod.swepub.kib.ki.se:136487070
http://kipublications.ki.se/Default.aspx?queryparsed=id:136487070URI
https://doi.org/10.1038/sdata.2017.112DOI

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Language:English
Summary in:English

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Subject category:art swepub-publicationtype

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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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Arakawa, T (author)
Fukuda, S (author)
Furuno, M (author)
Hasegawa, A (author)
Hori, F (author)
Ishikawa-Kato, S (author)
Kaida, K (author)
Kaiho, A (author)
Kanamori-Katayama, M (author)
Kawashima, T (author)
Kojima, M (author)
Kubosaki, A (author)
Manabe, RI (author)
Murata, M (author)
Nagao-Sato, S (author)
Nakazato, K (author)
Ninomiya, N (author)
Nishiyori-Sueki, H (author)
Noma, S (author)
Saijyo, E (author)
Saka, A (author)
Sakai, M (author)
Simon, C (author)
Suzuki, N (author)
Tagami, M (author)
Watanabe, S (author)
Yoshida, S (author)
Arner, PKarolinska Institutet (author)
Axton, RA (author)
Babina, M (author)
Baillie, JK (author)
Barnett, TC (author)
Beckhouse, AG (author)
Blumenthal, A (author)
Bodega, B (author)
Bonetti, A (author)
Briggs, J (author)
Brombacher, F (author)
Carlisle, AJ (author)
Clevers, HC (author)
Davis, CA (author)
Detmar, M (author)
Dohi, T (author)
Edge, ASB (author)
Edinger, M (author)
Ehrlund, A (author)
Ekwall, KKarolinska Institutet (author)
Endoh, M (author)
Enomoto, H (author)
Eslami, A (author)
Fagiolini, M (author)
Fairbairn, L (author)
Farach-Carson, MC (author)
Faulkner, GJ (author)
Ferrai, C (author)
Fisher, ME (author)
Forrester, LM (author)
Fujita, R (author)
Furusawa, J (author)
Geijtenbeek, TB (author)
Gingeras, T (author)
Goldowitz, D (author)
Guhl, S (author)
Guler, R (author)
Gustincich, S (author)
Ha, TJ (author)
Hamaguchi, M (author)
Hara, M (author)
Hasegawa, Y (author)
Herlyn, M (author)
Heutink, P (author)
Hitchens, KJ (author)
Hume, DA (author)
Ikawa, T (author)
Ishizu, Y (author)
Kai, C (author)
Kawamoto, H (author)
Kawamura, YI (author)
Kempfle, JS (author)
Kenna, TJ (author)
Kere, JKarolinska Institutet (author)
Khachigian, LM (author)
Kitamura, T (author)
Klein, S (author)
Klinken, SP (author)
Knox, AJ (author)
Kojima, S (author)
Koseki, H (author)
Koyasu, S (author)
Lee, W (author)
Lennartsson, AKarolinska Institutet (author)
Mackay-sim, A (author)
Mejhert, NKarolinska Institutet (author)
Mizuno, Y (author)
Morikawa, H (author)
Morimoto, M (author)
Moro, K (author)
Morris, KJ (author)
Motohashi, H (author)
Mummery, CL (author)
Nakachi, Y (author)
Nakahara, F (author)
Nakamura, T (author)
Nakamura, Y (author)
Nozaki, T (author)
Ogishima, S (author)
Ohkura, N (author)
Ohno, H (author)
Ohshima, M (author)
Okada-Hatakeyama, M (author)
Okazaki, Y (author)
Orlando, V (author)
Ovchinnikov, DA (author)
Passier, R (author)
Patrikakis, M (author)
Pombo, A (author)
Pradhan-Bhatt, S (author)
Qin, XY (author)
Rehli, M (author)
Rizzu, P (author)
Roy, S (author)
Sajantila, A (author)
Sakaguchi, S (author)
Sato, H (author)
Satoh, H (author)
Savvi, S (author)
Saxena, A (author)
Schmidl, C (author)
Schneider, C (author)
Schulze-Tanzil, GG (author)
Schwegmann, A (author)
Sheng, GJ (author)
Shin, JW (author)
Sugiyama, D (author)
Sugiyama, T (author)
Summers, KM (author)
Takahashi, N (author)
Takai, J (author)
Tanaka, H (author)
Tatsukawa, H (author)
Tomoiu, A (author)
Toyoda, H (author)
van de Wetering, M (author)
van den Berg, LM (author)
Verardo, R (author)
Vijayan, D (author)
Wells, CA (author)
Winteringham, LN (author)
Wolvetang, E (author)
Yamaguchi, Y (author)
Yamamoto, M (author)
Yanagi-Mizuochi, C (author)
Yoneda, M (author)
Yonekura, Y (author)
Zhang, PG (author)
Zucchelli, S (author)
Abugessaisa, I (author)
Arner, E (author)
Harshbarger, J (author)
Kondo, A (author)
Lassmann, T (author)
Lizio, M (author)
Sahin, S (author)
Sengstag, T (author)
Severin, J (author)
Shimoji, H (author)
Suzuki, M (author)
Suzuki, H (author)
Kawai, J (author)
Kondo, N (author)
Itoh, M (author)
Daub, CO (author)
Kasukawa, T (author)
Kawaji, H (author)
Carninci, P (author)
Forrest, ARR (author)
Hayashizaki, Y (author)
Karolinska Institutet (creator_code:org_t)

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By the author/editor: Noguchi, S; Arakawa, T; Fukuda, S; Furuno, M; Hasegawa, A; Hori, F; show more...; Ishikawa-Kato, S; Kaida, K; Kaiho, A; Kanamori-Katayam ...; Kawashima, T; Kojima, M; Kubosaki, A; Manabe, RI; Murata, M; Nagao-Sato, S; Nakazato, K; Ninomiya, N; Nishiyori-Sueki, ...; Noma, S; Saijyo, E; Saka, A; Sakai, M; Simon, C; Suzuki, N; Tagami, M; Watanabe, S; Yoshida, S; Arner, P; Axton, RA; Babina, M; Baillie, JK; Barnett, TC; Beckhouse, AG; Blumenthal, A; Bodega, B; Bonetti, A; Briggs, J; Brombacher, F; Carlisle, AJ; Clevers, HC; Davis, CA; Detmar, M; Dohi, T; Edge, ASB; Edinger, M; Ehrlund, A; Ekwall, K; Endoh, M; Enomoto, H; Eslami, A; Fagiolini, M; Fairbairn, L; Farach-Carson, M ...; Faulkner, GJ; Ferrai, C; Fisher, ME; Forrester, LM; Fujita, R; Furusawa, J; Geijtenbeek, TB; Gingeras, T; Goldowitz, D; Guhl, S; Guler, R; Gustincich, S; Ha, TJ; Hamaguchi, M; Hara, M; Hasegawa, Y; Herlyn, M; Heutink, P; Hitchens, KJ; Hume, DA; Ikawa, T; Ishizu, Y; Kai, C; Kawamoto, H; Kawamura, YI; Kempfle, JS; Kenna, TJ; Kere, J; Khachigian, LM; Kitamura, T; Klein, S; Klinken, SP; Knox, AJ; Kojima, S; Koseki, H; Koyasu, S; Lee, W; Lennartsson, A; Mackay-sim, A; Mejhert, N; Mizuno, Y; Morikawa, H; Morimoto, M; Moro, K; Morris, KJ; Motohashi, H; Mummery, CL; Nakachi, Y; Nakahara, F; Nakamura, T; Nakamura, Y; Nozaki, T; Ogishima, S; Ohkura, N; Ohno, H; Ohshima, M; Okada-Hatakeyama ...; Okazaki, Y; Orlando, V; Ovchinnikov, DA; Passier, R; Patrikakis, M; Pombo, A; Pradhan-Bhatt, S; Qin, XY; Rehli, M; Rizzu, P; Roy, S; Sajantila, A; Sakaguchi, S; Sato, H; Satoh, H; Savvi, S; Saxena, A; Schmidl, C; Schneider, C; Schulze-Tanzil, ...; Schwegmann, A; Sheng, GJ; Shin, JW; Sugiyama, D; Sugiyama, T; Summers, KM; Takahashi, N; Takai, J; Tanaka, H; Tatsukawa, H; Tomoiu, A; Toyoda, H; van de Wetering, ...; van den Berg, LM; Verardo, R; Vijayan, D; Wells, CA; Winteringham, LN; Wolvetang, E; Yamaguchi, Y; Yamamoto, M; Yanagi-Mizuochi, ...; Yoneda, M; Yonekura, Y; Zhang, PG; 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, CO; Kasukawa, T; Kawaji, H; Carninci, P; Forrest, ARR; Hayashizaki, Y; show less...

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