TY  - JOUR
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
Y1  - 2009/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 255 
EP  - 265 
DO  - 10.1101/gr.084541.108 
VL  - 19 
IS  - 2 
UR  - http://genome.cshlp.org/content/19/2/255.abstract 
N2  - 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. 
ER  -