RT Journal Article SR Electronic T1 Linking FANTOM5 CAGE peaks to annotations with CAGEscan JF bioRxiv FD Cold Spring Harbor Laboratory SP 126474 DO 10.1101/126474 A1 Nicolas Bertin A1 Mickaël Mendez A1 Akira Hasegawa A1 Marina Lizio A1 Imad Abugessaisa A1 Jessica Severin A1 Mizuho Sakai-Ohno A1 Timo Lassmann A1 Takeya Kasusawa A1 Hideya Kawaji A1 Yoshihide Hayashizaki A1 Alistair R. R. Forrest A1 Piero Carninci A1 Charles Plessy YR 2017 UL http://biorxiv.org/content/early/2017/04/11/126474.abstract AB The FANTOM5 expression atlas is a quantitative measurement of the activity of nearly 200,000 promoter regions across nearly 2,000 different human primary cells, tissue types and cell lines. Generation of this atlas was made possible by the use of CAGE, an experimental approach to localise transcription start sites at single-nucleotide resolution by sequencing the 5′ ends of capped RNAs after their conversion to cDNAs. While 50% of CAGE-defined promoter regions could be confidently associated to adjacent transcriptional units, nearly 100,000 promoter regions remained gene-orphan. To address this, we used the CAGEscan method, in which random-primed 5′-cDNAs are paired-end sequenced. Pairs starting in the same region are assembled in transcript models called CAGEscan clusters. Here, we present the production and quality control of CAGEscan libraries from 56 FANTOM5 RNA sources, which enhances the FANTOM5 expression atlas by providing experimental evidence associating core promoter regions with their cognate transcripts.