FANTOM5 CAGE profiles of human and mouse samples
Shuhei Noguchi,Takahiro Arakawa,Shiro Fukuda,Masaaki Furuno,Akira Hasegawa,Fumi Hori,Sachi Ishikawa-Kato,Kaoru Kaida,Ai Kaiho,Mutsumi Kanamori-Katayama,Tsugumi Kawashima,Miki Kojima,Atsutaka Kubosaki,Ri Ichiroh Manabe,Mitsuyoshi Murata,Sayaka Nagao-Sato,Kenichi Nakazato,Noriko Ninomiya,Hiromi Nishiyori-Sueki,Shohei Noma,Eri Saijyo,Akiko Saka,Mizuho Sakai,Christophe Simon,Naoko Suzuki,Michihira Tagami,Shoko Watanabe,Shigehiro Yoshida,Peter Arner,Richard A Axton,Magda Babina,J Kenneth Baillie,Timothy C. Barnett,Anthony G Beckhouse,Antje Blumenthal,Beatrice Bodega,Alessandro Bonetti,James Briggs,Frank Brombacher,Frank Brombacher,Ailsa J Carlisle,Hans Clevers,Hans Clevers,Carrie A. Davis,Michael Detmar,Taeko Dohi,B. Albert S. Edge,Matthias Edinger,Anna Ehrlund,Karl Ekwall,Mitsuhiro Endoh,Hideki Enomoto,Afsaneh Eslami,Michela Fagiolini,Lynsey Fairbairn,Mary C. Farach-Carson,Geoffrey J. Faulkner,Carmelo Ferrai,Malcolm E. Fisher,Lesley M. Forrester,Rie Fujita,Jun Ichi Furusawa,Teunis B. H. Geijtenbeek,Thomas R. Gingeras,Dan Goldowitz,Sven Guhl,Reto Guler,Reto Guler,Stefano Gustincich,Stefano Gustincich,Thomas J. Ha,Masahide Hamaguchi,Mitsuko Hara,Yuki Hasegawa,Meenhard Herlyn,Peter Heutink,Kelly J Hitchens,David A. Hume,Tomokatsu Ikawa,Yuri Ishizu,Chieko Kai,Hiroshi Kawamoto,Yuki I. Kawamura,Judith S. Kempfle,Tony J. Kenna,Juha Kere,Juha Kere,Levon M. Khachigian,Toshio Kitamura,Sarah Klein,S. Peter Klinken,Alan J. Knox,Soichi Kojima,Haruhiko Koseki,Shigeo Koyasu,Weon Ju Lee,Andreas Lennartsson,Alan Mackay-Sim,Niklas Mejhert,Yosuke Mizuno,Hiromasa Morikawa,Mitsuru Morimoto,Kazuyo Moro,Kelly J. Morris,Hozumi Motohashi,Christine L. Mummery,Yutaka Nakachi,Yutaka Nakachi,Fumio Nakahara,Toshiyuki Nakamura,Yukio Nakamura,Tadasuke Nozaki,Soichi Ogishima,Naganari Ohkura,Hiroshi Ohno,Mitsuhiro Ohshima,Mariko Okada-Hatakeyama,Yasushi Okazaki,Valerio Orlando,Dmitry A. Ovchinnikov,Robert Passier,Margaret Patrikakis,Ana Pombo,Swati Pradhan-Bhatt,Xian-Yang Qin,Michael Rehli,Patrizia Rizzu,Sugata Roy,Antti Sajantila,Shimon Sakaguchi,Hiroki Sato,Hironori Satoh,Suzana Savvi,Suzana Savvi,Alka Saxena,Christian Schmidl,Claudio Schneider,Gundula Schulze-Tanzil,Anita Schwegmann,Anita Schwegmann,Guojun Sheng,Jay W. Shin,Daisuke Sugiyama,Takaaki Sugiyama,Kim M. Summers,Naoko Takahashi,Jun Takai,Hiroshi Tanaka,Hideki Tatsukawa,Andru Tomoiu,Hiroo Toyoda,Marcvande Wetering,Linda M. van den Berg,Roberto Verardo,Dipti Vijayan,Christine A. Wells,Louise N. Winteringham,Ernst J. Wolvetang,Yoko Yamaguchi,Masayuki Yamamoto,Chiyo Yanagi-Mizuochi,Misako Yoneda,Yohei Yonekura,Peter G. Zhang,Silvia Zucchelli,Imad Abugessaisa,Erik Arner,Jayson Harshbarger,Atsushi Kondo,Timo Lassmann,Marina Lizio,Serkan Sahin,Thierry Sengstag,Jessica Severin,Hisashi Shimoji,Masanori Suzuki,Harukazu Suzuki,Jun Kawai,Naoto Kondo,Masayoshi Itoh,Carsten O. Daub,Takeya Kasukawa,Hideya Kawaji,Piero Carninci,Alistair R. R. Forrest,Yoshihide Hayashizaki +185 more
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TLDR
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 coupled with single-molecule sequencing to represent the consequence of transcriptional regulation in each analyzed state of mammalian cells.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.read more
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PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.
TL;DR: An online database, PanglaoDB, accessible through a user-friendly interface that can be used to explore published mouse and human single cell RNA sequencing studies, and establishes a community-curated cell-type marker compendium, containing more than 6000 gene-cell-type associations, as a resource for automatic annotation of cell types.
Journal ArticleDOI
An atlas of the protein-coding genes in the human, pig, and mouse brain
Evelina Sjöstedt,Evelina Sjöstedt,Wen Zhong,Linn Fagerberg,Max J. Karlsson,Nicholas Mitsios,Csaba Adori,Per Oksvold,Fredrik Edfors,Agnieszka Limiszewska,Feria Hikmet,Jinrong Huang,Yutao Du,Lin Lin,Zhanying Dong,Ling Yang,Xin Liu,Hui Jiang,Xun Xu,Jian Wang,Huanming Yang,Lars Bolund,Adil Mardinoglu,Cheng Zhang,Kalle von Feilitzen,Cecilia Lindskog,Fredrik Pontén,Yonglun Luo,Tomas Hökfelt,Mathias Uhlén,Mathias Uhlén,Jan Mulder +31 more
TL;DR: A comprehensive molecular dissection of the main regions of the human, pig, and mouse brain using transcriptomics and antibody-based mapping suggests similar regional organization and expression patterns in the three mammalian species, consistent with the view that basic brain architecture is preserved during mammalian evolution.
Journal ArticleDOI
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases.
Marina Lizio,Imad Abugessaisa,Shuhei Noguchi,Atsushi Kondo,Akira Hasegawa,Chung-Chau Hon,Michiel J. L. de Hoon,Jessica Severin,Shinya Oki,Yoshihide Hayashizaki,Piero Carninci,Takeya Kasukawa,Hideya Kawaji +12 more
TL;DR: The recent updates of both data and interfaces in the FANTOM web resource are reported, including expansion of the resource by employing different assays, which yielded additional atlases of long noncoding RNAs, miRNAs and their promoters.
Journal ArticleDOI
Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA
Jin Wang,Jin Wang,Bing Liang Alvin Chew,Bing Liang Alvin Chew,Yong Lai,Hongping Dong,Luang Xu,Seetharamsingh Balamkundu,Seetharamsingh Balamkundu,Weiling Maggie Cai,Weiling Maggie Cai,Liang Cui,Chuan-Fa Liu,Xin-Yuan Fu,Zhenguo Lin,Pei Yong Shi,Timothy K. Lu,Timothy K. Lu,Dahai Luo,Samie R. Jaffrey,Peter C. Dedon,Peter C. Dedon +21 more
TL;DR: Applying CapQuant to RNA from purified dengue virus, Escherichia coli, yeast, mouse tissues, and human cells, it is reported that CapQuant accurately captured the preference for purine nucleotides at eukaryotic transcription start sites and the correlation between metabolite levels and metabolite caps.
Journal ArticleDOI
A joint NCBI and EMBL-EBI transcript set for clinical genomics and research
Joannella Morales,Shashikant Pujar,Jane E. Loveland,Alexander Astashyn,Ruth Bennett,Andrew Berry,Eric Cox,R. Davidson,Olga Ermolaeva,Catherine M. Farrell,Reham Fatima,Laurent Gil,Tamara Goldfarb,José M. González,Diana Haddad,Matthew P. Hardy,Toby Hunt,John D. Jackson,Vinita Joardar,M. Kay,Vamsi K Kodali,Kelly M. McGarvey,Aoife McMahon,Jonathan M. Mudge,Daniel N. Murphy,Michael R. Murphy,Bhanu Rajput,Sanjida H. Rangwala,Lillian D. Riddick,Françoise Thibaud-Nissen,Glen Threadgold,Anjana Raina Vatsan,Craig Wallin,David Webb,Paul Flicek,Ewan Birney,Kim D. Pruitt,Adam Frankish,Fiona Cunningham,Terence Murphy +39 more
TL;DR: The Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration as mentioned in this paper is a set of transcripts and corresponding proteins annotated for each human protein-coding gene.
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TL;DR: Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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