FANTOM5 CAGE profiles of human and mouse samples

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.

Citation

Noguchi S, Arakawa T, Fukuda S, Furuno M, Hasegawa A, et al. (2017) FANTOM5 CAGE profiles of human and mouse samples. Scientific Data 4: 170112. Available: http://dx.doi.org/10.1038/sdata.2017.112.

Relations

Is Supplemented By:

[Dataset]
Clevers, H., Edge, A., Wetering, M. V. D., Detmar, M., Koseki, H., Edinger, M., Ekwall, K., Hume, D. A., Axton, R. A., Hara, M., Kitamura, T., Hasegawa, Y., Takahashi, N., Carninci, P., Wolvetang, E. J., Ovchinnikov, D., Davis, C., Hideya Kawaji, Gingeras, T., … Morikawa, H. (2017). FANTOM5 CAGE profiles of human and mouse samples. Figshare. https://doi.org/10.6084/M9.FIGSHARE.C.3728767.V1. DOI: 10.6084/m9.figshare.c.3728767.v1 Handle: 10754/664213
[Software]
Title: hkawaji/dpi1: Decomposition-based peak identification, which find peaks across a large number of TSS (transcription starting site) profiles. Publication Date: 2013-12-25. github: hkawaji/dpi1 Handle: 10754/667011

Collections

Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Bioscience Program

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Except where otherwise noted, this item's license is described as This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files made available in this article.