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Series GSE125696 Query DataSets for GSE125696
Status Public on Jul 29, 2019
Title REV-ERBa and REV-ERBb function as key factors regulating Mammalian Circadian Output
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The circadian clock regulates behavioural and physiological processes in a 24-h cycle. The nuclear receptors REV-ERBa and REV-ERBb are involved in the cell-autonomous circadian transcriptional/translational feedback loops as transcriptional repressors. A number of studies have also demonstrated a pivotal role of REV-ERBs in regulation of metabolic, neuronal, and inflammatory functions including bile acid metabolism, lipid metabolism, and production of inflammatory cytokines. Given the multifunctional role of REV-ERBs, it is important to elucidate the mechanism through which REV-ERBs exert their functions. To this end, we established a Rev-erba/Rev-erbb double-knockout mouse embryonic stem (ES) cell model and analyzed the circadian clock and clock-controlled output gene expressions. A comprehensive mRNA-seq analysis revealed that the complete knockout of both Rev-erba and Rev-erbb does not abrogate expression rhythms of E-box-regulated core clock genes but drastically changes a diverse set of other rhythmically-expressed output genes. Of note, REV-ERBa/b deficiency does not compromise circadian expression rhythms of PER2, while REV-ERB target genes, Bmal1 and Npas2, are significantly upregulated. This study emphasizes REV-ERBs function to form an essential link between the circadian clock and a wide variety of cellular physiological functions.
Overall design Control (WT) and Rev-erba/Rev-erbb deficient (KO) mouse ES cells on Per2::Luciferase knock-in background were differentiated for 28 days upon embryoid body formation, treated with 100 nM dexamethasone, and subjected to RNA extraction at 4-h intervals from 12 h to 56 h after dexamethasone stimulation.
Contributor(s) Tsuchiya Y, Koike N, Yagita K
Citation(s) 31308426
Submission date Jan 25, 2019
Last update date Jul 29, 2019
Contact name Kazuhiro Yagita
Organization name Kyoto Prefectural University of Medicine
Street address Kawaramachi-Hirokoji, Kamigyo-ku
City Kyoto
ZIP/Postal code 602-8566
Country Japan
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (24)
GSM3580497 WT_12h
GSM3580498 WT_16h
GSM3580499 WT_20h
BioProject PRJNA517181
SRA SRP182101

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Supplementary file Size Download File type/resource
GSE125696_RAW.tar 2.4 Gb (http)(custom) TAR (of BW)
GSE125696_RevErbKOcells_RNAseq_knownCanonical2016_exon_RPKM_annotation.txt.gz 5.4 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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