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Series GSE39978 Query DataSets for GSE39978
Status Public on Aug 31, 2012
Title Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The mammalian circadian clock involves a transcriptional feedback loop in which CLOCK and BMAL1 activate the Period and Cryptochrome genes, which then feedback and repress their own transcription. We have interrogated the transcriptional architecture of the circadian transcriptional regulatory loop on a genome scale in mouse liver and find a stereotyped, time-dependent pattern of transcription factor binding, RNA polymerase II (RNAPII) recruitment, RNA expression and chromatin states. We find that the circadian transcriptional cycle of the clock consists of three distinct phases — a poised state, a coordinated de novo transcriptional activation state, and a repressed state. Interestingly only 22% of mRNA cycling genes are driven by de novo transcription, suggesting that both transcriptional and post-transcriptional mechanisms underlie the mammalian circadian clock. We also find that circadian modulation of RNAPII recruitment and chromatin remodeling occurs on a genome-wide scale far greater than that seen previously by gene expression profiling.
 
Overall design Examination of whole transcriptome every 4hr during the circadian cycle in mouse liver
 
Contributor(s) Koike N, Yoo S, Huang H, Kumar V, Lee C, Kim T, Takahashi JS
Citation(s) 22936566
Submission date Aug 08, 2012
Last update date May 15, 2019
Contact name Joseph S Takahashi
E-mail(s) [email protected]
Phone 214-648-1876
Organization name University of Texas Southwestern Medical Center
Department HHMI, Neuroscience
Lab Joseph S. Takahashi
Street address 5323 Harry Hines Blvd., NA4.118
City Dallas
State/province TX
ZIP/Postal code 75390-9111
Country USA
 
Platforms (1)
GPL14602 AB SOLiD 4 System (Mus musculus)
Samples (12)
GSM982826 Sample 1_whole transcriptome (RNA-seq)
GSM982827 Sample 2_whole transcriptome (RNA-seq)
GSM982828 Sample 3_whole transcriptome (RNA-seq)
This SubSeries is part of SuperSeries:
GSE39860 Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals
Relations
BioProject PRJNA172198
SRA SRP014751

Download family Format
SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE39978_RAW.tar 2.9 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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