RT Journal
A1 Valen, Eivind
A1 Pascarella, Giovanni
A1 Chalk, Alistair
A1 Maeda, Norihiro
A1 Kojima, Miki
A1 Kawazu, Chika
A1 Murata, Mitsuyoshi
A1 Nishiyori, Hiromi
A1 Lazarevic, Dejan
A1 Motti, Dario
A1 Marstrand, Troels Torben
A1 Tang, Man-Hung Eric
A1 Zhao, Xiaobei
A1 Krogh, Anders
A1 Winther, Ole
A1 Arakawa, Takahiro
A1 Kawai, Jun
A1 Wells, Christine
A1 Daub, Carsten
A1 Harbers, Matthias
A1 Hayashizaki, Yoshihide
A1 Gustincich, Stefano
A1 Sandelin, Albin
A1 Carninci, Piero
T1 Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
JF Genome Research 
JO Genome Research 
YR 2009 
FD February 01 
VO 19 
IS 2 
SP 255 
OP 265 
DO 10.1101/gr.084541.108 
UL http://genome.cshlp.org/content/19/2/255.abstract 
AB Finding and characterizing mRNAs, their transcription start sites (TSS), and their associated promoters is a major focus in post-genome biology. Mammalian cells have at least 5–10 magnitudes more TSS than previously believed, and deeper sequencing is necessary to detect all active promoters in a given tissue. Here, we present a new method for high-throughput sequencing of 5′ cDNA tags—DeepCAGE: merging the Cap Analysis of Gene Expression method with ultra-high-throughput sequence technology. We apply DeepCAGE to characterize 1.4 million sequenced TSS from mouse hippocampus and reveal a wealth of novel core promoters that are preferentially used in hippocampus: This is the most comprehensive promoter data set for any tissue to date. Using these data, we present evidence indicating a key role for the Arnt2 transcription factor in hippocampus gene regulation. DeepCAGE can also detect promoters used only in a small subset of cells within the complex tissue.