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.
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@article{noguchi_fantom5_2017,
title = {FANTOM5 CAGE profiles of human and mouse samples},
author = {Noguchi, Shuhei and Arakawa, Takahiro and Fukuda, Shiro and Furuno, Masaaki and Hasegawa, Akira and Hori, Fumi and Ishikawa-Kato, Sachi and Kaida, Kaoru and Kaiho, Ai and Kanamori-Katayama, Mutsumi and Kawashima, Tsugumi and Kojima, Miki and Kubosaki, Atsutaka and Manabe, Ri-ichiroh and Murata, Mitsuyoshi and Nagao-Sato, Sayaka and Nakazato, Kenichi and Ninomiya, Noriko and Nishiyori-Sueki, Hiromi and Noma, Shohei and Saijyo, Eri and Saka, Akiko and Sakai, Mizuho and Simon, Christophe and Suzuki, Naoko and Tagami, Michihira and Watanabe, Shoko and Yoshida, Shigehiro and Arner, Peter and Axton, Richard A. and Babina, Magda and Baillie, J. Kenneth and Barnett, Timothy C. and Beckhouse, Anthony G. and Blumenthal, Antje and Bodega, Beatrice and Bonetti, Alessandro and Briggs, James and Brombacher, Frank and Carlisle, Ailsa J. and Clevers, Hans C. and Davis, Carrie A. and Detmar, Michael and Dohi, Taeko and Edge, Albert S. B. and Edinger, Matthias and Ehrlund, Anna and Ekwall, Karl and Endoh, Mitsuhiro and Enomoto, Hideki and Eslami, Afsaneh and Fagiolini, Michela and Fairbairn, Lynsey and Farach-Carson, Mary C. and Faulkner, Geoffrey J.},
doi = {10.1038/sdata.2017.112},
issn = {2052-4463},
year = {2017},
date = {2017-08-29},
journal = {Scientific Data},
volume = {4},
pages = {170112},
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.},
keywords = {Faulknerlab},
pubstate = {published},
tppubtype = {article}
}