Data Descriptor: FANTOM5 CAGE profiles of human and mouse samples

被引：178

作者：

Noguchi, Shuhei ^{[1
]}

Arakawa, Takahiro ^{[1
,2
]}

Fukuda, Shiro ^{[2
]}

Furuno, Masaaki ^{[1
,2
]}

Hasegawa, Akira ^{[1
,2
]}

Hori, Fumi ^{[1
,2
]}

Ishikawa-Kato, Sachi ^{[1
,2
]}

Kaida, Kaoru ^{[2
]}

Kaiho, Ai ^{[2
]}

Kanamori-Katayama, Mutsumi ^{[2
]}

Kawashima, Tsugumi ^{[1
,2
]}

Kojima, Miki ^{[1
,2
]}

Kubosaki, Atsutaka ^{[2
]}

Manabe, Ri-ichiroh ^{[1
,2
]}

Murata, Mitsuyoshi ^{[1
,2
]}

Nagao-Sato, Sayaka ^{[1
,2
]}

Nakazato, Kenichi ^{[2
]}

Ninomiya, Noriko ^{[2
]}

Nishiyori-Sueki, Hiromi ^{[1
,2
]}

Noma, Shohei ^{[1
,2
]}

Saijyo, Eri ^{[2
]}

Saka, Akiko ^{[2
]}

Sakai, Mizuho ^{[1
,2
]}

Simon, Christophe ^{[2
]}

Suzuki, Naoko ^{[1
,2
]}

Tagami, Michihira ^{[1
,2
]}

Watanabe, Shoko ^{[1
,2
]}

Yoshida, Shigehiro ^{[2
]}

Arner, Peter ^{[3
,4
]}

Axton, Richard A. ^{[5
]}

Babina, Magda ^{[6
]}

Baillie, J. Kenneth ^{[7
,8
]}

Barnett, Timothy C. ^{[9
,10
]}

Beckhouse, Anthony G. ^{[11
]}

Blumenthal, Antje ^{[12
]}

Bodega, Beatrice ^{[13
]}

Bonetti, Alessandro ^{[1
,2
]}

Briggs, James ^{[14
]}

Brombacher, Frank ^{[15
,16
,17
]}

Carlisle, Ailsa J. ^{[7
,8
]}

Clevers, Hans C. ^{[18
,19
]}

Davis, Carrie A. ^{[20
]}

Detmar, Michael ^{[21
]}

Dohi, Taeko ^{[22
]}

Edge, Albert S. B. ^{[23
]}

Edinger, Matthias ^{[24
,25
]}

Ehrlund, Anna ^{[3
,4
]}

Ekwall, Karl ^{[26
]}

Endoh, Mitsuhiro ^{[27
]}

Enomoto, Hideki ^{[28
]}

机构：

[1] RIKEN Ctr Life Sci Technol, Div Genom Technol, Yokohama, Kanagawa 2300045, Japan

[2] RIKEN Omics Sci Ctr, Yokohama, Kanagawa 2300045, Japan

[3] Karolinska Inst, Dept Med, S-14186 Stockholm, Sweden

[4] Karolinska Univ Hosp, Ctr Metab & Endocrinol, S-14186 Stockholm, Sweden

[5] Univ Edinburgh, Scottish Ctr Regenerat Med, 5 Little France Dr, Edinburgh EH16 4UU, Midlothian, Scotland

[6] Charite Univ Med Berlin, Dept Dermatol & Allergy, Charitepl 1, D-10117 Berlin, Germany

[7] Univ Edinburgh, Roslin Inst, Edinburgh EH25 9RG, Midlothian, Scotland

[8] Univ Edinburgh, Royal Dick Sch Vet Studies, Edinburgh EH25 9RG, Midlothian, Scotland

[9] Univ Queensland, Australian Infect Dis Res Ctr, St Lucia, Qld 4072, Australia

[10] Univ Queensland, Sch Chem & Mol Biosci, St Lucia, Qld 4072, Australia

[11] Biorad Labs Pty Ltd, Hercules, CA 94547 USA

[12] Univ Queensland, Diamantina Inst, Woolloongabba, Qld 4102, Australia

[13] IRCCS Fdn Santa Lucia, Via Fosso di Fiorano 64, I-00143 Rome, Italy

[14] Univ Queensland, Australian Inst Bioengn & Nanotechnol AIBN, St Lucia, Qld 4072, Australia

[15] Univ Cape Town, Inst Infect Dis & Mol Med IDM, Div Immunol, Anzio Rd, Cape Town, South Africa

[16] Univ Cape Town, South African Med Res Council SAMRC, Immunol Infect Dis, Fac Hlth Sci, Anzio Rd,Observ 7925, Cape Town, South Africa

[17] Cape Town Component, Int Ctr Genet Engn & Biotechnol, Anzio Rd,Observ 7925, Cape Town, South Africa

[18] Royal Netherlands Acad Arts & Sci, Hubrecht Inst, Uppsalalaan 8, NL-3584 CT Utrecht, Netherlands

[19] Univ Med Ctr Utrecht, Postbus 85500, NL-3508 GA Utrecht, Netherlands

[20] Cold Spring Harbor Lab, Genom, Cold Spring Harbor, NY 11797 USA

[21] Swiss Fed Inst Technol, Inst Pharmaceut Sci, Vladimir Prelog Weg 3,HCI H 303, CH-8093 Zurich, Switzerland

[22] Natl Ctr Global Hlth & Med, Res Ctr Hepatitis & Immunol, Gastroenterol, Res Inst, Ichikawa, Chiba 2728516, Japan

[23] Harvard Med Sch, Dept Otol & Laryngol, Boston, MA 02114 USA

[24] Univ Hosp Regensburg, Dept Internal Med 3, FJ Strauss Allee 11, D-93053 Regensburg, Germany

[25] Univ Hosp Regensburg, RCI Regensburg Ctr Intervent Immunol, FJ Strauss Allee 11, D-93053 Regensburg, Germany

[26] Karolinska Inst, Dept Biosci & Nutr, Halsovagen 7-9, SE-14183 Huddinge, Sweden

[27] RIKEN Ctr Integrat Med Sci, Yokohama, Kanagawa 2300045, Japan

[28] RIKEN Ctr Dev Biol, Lab Neuronal Differentiat & Regenerat, Chuou Ku, Kobe, Hyogo 6500047, Japan

[29] Tokyo Med & Dent Univ, Med Res Inst, Dept Bioinformat, Bunkyo Ku, Tokyo 1138510, Japan

[30] Harvard Med Sch, Childrens Hosp, FM Kirby Neurobiol Ctr, Boston, MA 02115 USA

[31] Univ Texas Hlth Sci Ctr, Houston, TX 77251 USA

[32] Mater Med Res Inst, Canc Biol Program, South Brisbane, Qld 4101, Australia

[33] Max Delbrueck Ctr, Berlin Inst Med Syst Biol, Robert Roessle Str 10, D-13125 Berlin, Germany

[34] Tohoku Univ, Dept Med Biochem, Grad Sch Med, Sendai, Miyagi 9808575, Japan

[35] Univ Amsterdam, Acad Med Ctr, Expt Immunol, Meibergdreef 9, NL-1105 AZ Amsterdam, Netherlands

[36] Univ British Columbia, Child & Family Res Inst, Ctr Mol Med & Therapeut, Dept Med Genet, Vancouver, BC V5Z 4H4, Canada

[37] SISSA, Neurosci, Via Bonomea 265, I-34136 Trieste, Italy

[38] Italian Istitute Technol, Dept Neurosci & Brian Technol, Via Morego 30, Genoa, Italy

[39] Osaka Univ, World Premier Int Immunol Frontier Res Ctr, Dept Expt Immunol, Suita, Osaka 5650871, Japan

[40] RIKEN Ctr Life Sci Technol, Wako, Saitama 3510198, Japan

[41] Melanoma Res Ctr, Wistar Inst, Philadelphia, PA 19104 USA

[42] German Ctr Neurodegenerat Dis DZNE Tubingen, Otfried Muller Str 23, D-72076 Tubingen, Germany

[43] Univ Tokyo, Inst Med Sci, Lab Anim Res Ctr, Minato Ku, Tokyo 1088639, Japan

[44] Univ Tokyo, Inst Med Sci, Int Res Ctr Infect Dis, Minato Ku, Tokyo 1088639, Japan

[45] Queensland Univ Technol, Translat Res Inst, Princess Alexandra Hosp, Inst Hlth & Biomed Innovat, Brisbane, Qld 4102, Australia

[46] Kings Coll London, Dept Genet & Mol Med, Guys St Thomas St, London, England

[47] Univ New S Wales, Ctr Vasc Res, Sydney, NSW 2052, Australia

[48] Univ New S Wales, Sch Med Sci, Vasc Biol & Translat Res, Sydney, NSW 2052, Australia

[49] Univ Tokyo, Inst Med Sci, Div Cellular Therapy, Minato Ku, Tokyo 1088639, Japan

[50] Univ Tokyo, Inst Med Sci, Div Stem Cell Signaling, Minato Ku, Tokyo 1088639, Japan

来源：

SCIENTIFIC DATA | 2017年 / 4卷

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

GENE-EXPRESSION; CELL-TYPES; TRANSCRIPTION; VISUALIZATION; ENHANCERS; GROWTH; ATLAS;

D O I：

10.1038/sdata.2017.112

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：10

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