Dataset Information

FANTOM5 CAGE profiles of human and mouse samples.

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.

SUBMITTER: Noguchi S

PROVIDER: S-EPMC5574368 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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FANTOM5 CAGE profiles of human and mouse samples.

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

Scientific data 20170829

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 ...[more]

PMID: 28850106

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Project description:BackgroundRespiratory infections such as influenza account for significant global mortality each year. Generating lipid profiles is a novel and emerging research approach that may provide new insights regarding the development and progression of priority respiratory infections. We hypothesized that select clusters of lipids in human sputum would be associated with specific viral infections (Influenza (H1N1, H3N2) or Rhinovirus).MethodsLipid identification and semi-quantitation was determined with liquid chromatography and high-resolution mass spectrometry in induced sputum from individuals with confirmed respiratory infections (influenza (H1N1, H3N2) or rhinovirus). Clusters of lipid species and associations between lipid profiles and the type of respiratory viral agent was determined using Bayesian profile regression and multinomial logistic regression.ResultsMore than 600 lipid compounds were identified across the sputum samples with the most abundant lipid classes identified as triglycerides (TG), phosphatidylethanolamines (PE), phosphatidylcholines (PC), Sphingomyelins (SM), ether-PC, and ether-PE. A total of 12 lipid species were significantly different when stratified by infection type and included acylcarnitine (AcCar) (10:1, 16:1, 18:2), diacylglycerols (DG) (16:0_18:0, 18:0_18:0), Lysophosphatidylcholine (LPC) (12:0, 20:5), PE (18:0_18:0), and TG (14:1_16:0_18:2, 15:0_17:0_19:0, 16:0_17:0_18:0, 19:0_19:0_19:0). Cluster analysis yielded three clusters of lipid profiles that were driven by just 10 lipid species (TGs and DGs). Cluster 1 had the highest levels of each lipid species and the highest prevalence of influenza A H3 infection (56%, n = 5) whereas cluster 3 had lower levels of each lipid species and the highest prevalence of rhinovirus (60%; n = 6). Using cluster 3 as the reference group, the crude odds of influenza A H3 infection compared to rhinovirus in cluster 1 was significantly (p = 0.047) higher (OR = 15.00 [95% CI: 1.03, 218.29]). After adjustment for confounders (smoking status and pulmonary comorbidities), the odds ratio (OR) became only marginally significant (p = 0.099), but the magnitude of the effect estimate was similar (OR = 16.00 [0.59, 433.03]).ConclusionsIn this study, human sputum lipid profiles were shown to be associated with distinct types of viral infection. Better understanding the relationship between respiratory infections of global importance and lipids contributes to advancing knowledge of pathogenesis of infections including identifying populations with increased susceptibility and developing effective therapeutics and biomarkers of health status.

Dataset Information

FANTOM5 CAGE profiles of human and mouse samples.

Publications

FANTOM5 CAGE profiles of human and mouse samples.

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