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Series GSE54651 Query DataSets for GSE54651
Status Public on Sep 30, 2014
Title A circadian gene expression atlas in mammals assayed by RNA-seq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary To characterize the role of the circadian clock in mouse physiology and behavior, we used RNA-seq and DNA arrays to quantify the transcriptomes of 12 mouse organs over time. We found 43% of all protein coding genes showed circadian rhythms in transcription somewhere in the body, largely in an organ-specific manner. In most organs, we noticed the expression of many oscillating genes peaked during transcriptional “rush hours” preceding dawn and dusk. Looking at the genomic landscape of rhythmic genes, we saw that they clustered together, were longer, and had more spliceforms than nonoscillating genes. Systems-level analysis revealed intricate rhythmic orchestration of gene pathways throughout the body. We also found oscillations in the expression of more than 1,000 known and novel noncoding RNAs (ncRNAs). Supporting their potential role in mediating clock function, ncRNAs conserved between mouse and human showed rhythmic expression in similar proportions as protein coding genes. Importantly, we also found that the majority of best-selling drugs and World Health Organization essential medicines directly target the products of rhythmic genes. Many of these drugs have short half-lives and may benefit from timed dosage. In sum, this study highlights critical, systemic, and surprising roles of the mammalian circadian clock and provides a blueprint for advancement in chronotherapy.
Overall design 96 samples total covering 12 different tissues, with no replicates. Each tissue sampled every 6 hours for 2 days (8 samples per tissue).
Contributor(s) Zhang R, Lahens NF, Ballance HI, Hughes ME, Hogenesch JB
Citation(s) 25349387
Submission date Feb 04, 2014
Last update date May 15, 2019
Contact name Nicholas Lahens
Organization name University of Pennsylvania
Department ITMAT
Street address Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (96)
GSM1321278 Adr_CT22
GSM1321279 Adr_CT28
GSM1321280 Adr_CT34
This SubSeries is part of SuperSeries:
GSE54652 A circadian gene expression atlas in mammals: Implications for biology and medicine
BioProject PRJNA237293
SRA SRP036186

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE54651_Adr_quant.txt.gz 1.1 Mb (ftp)(http) TXT
GSE54651_Aor_quant.txt.gz 1.0 Mb (ftp)(http) TXT
GSE54651_BFat_quant.txt.gz 947.1 Kb (ftp)(http) TXT
GSE54651_Bstm_quant.txt.gz 1.1 Mb (ftp)(http) TXT
GSE54651_Cer_quant.txt.gz 1.1 Mb (ftp)(http) TXT
GSE54651_Hrt_quant.txt.gz 962.9 Kb (ftp)(http) TXT
GSE54651_Hyp_quant.txt.gz 1.1 Mb (ftp)(http) TXT
GSE54651_Kid_quant.txt.gz 1.0 Mb (ftp)(http) TXT
GSE54651_Liv_quant.txt.gz 955.0 Kb (ftp)(http) TXT
GSE54651_Lun_quant.txt.gz 1.1 Mb (ftp)(http) TXT
GSE54651_Mus_quant.txt.gz 926.7 Kb (ftp)(http) TXT
GSE54651_RAW.tar 170.6 Mb (http)(custom) TAR (of TAB)
GSE54651_WFat_quant.txt.gz 1.1 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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