GEO DataSets

Analysis of livers of C57BL/6J animals after 10 weeks on a high fat diet (HFD). Livers were harvested every 4 hours up to Zeitgeber time 20. Circadian rhythms and cellular metabolism are intimately linked. Results provide insight into the molecular effect of HFD on the circadian clock.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 protocol, 6 time sets

Platform:

GPL6246

Series:

GSE52333

36 Samples

Download data: CEL, CHP

(Submitter supplied) The liver circadian clock is reprogrammed by nutritional challenge through the rewiring of specific transcriptional pathways. As the gut microbiota is tightly connected to host metabolism, whose coordination is governed by the circadian clock, we explored whether gut microbes influence circadian homeostasis and how they distally control the peripheral clock in the liver. Using fecal transplant procedures we reveal that, in response to high fat diet, the gut microbiota drives PPARγ-mediated activation of newly oscillatory transcriptional programs in the liver. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

48 Samples

Download data: CEL, XLS

(Submitter supplied) Circadian and metabolic processes are codependent. This experiment was designed to understand how a high fat diet affects circadian gene expression in the liver. Circadian gene expression in the liver is necessary for energy balance.

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4783

Platform:

GPL6246

36 Samples

Download data: CEL, CHP

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14602

12 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14602 GPL15907

138 Samples

Download data: BED, BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14602 GPL15907

150 Samples

Download data: BED, BW

(Submitter supplied) The mammalian circadian clock relies on the master genes CLOCK (CLK) and BMAL1 and drives rhythmic gene expression to regulate biological functions under circadian control. We recently uncovered a surprising disconnect between the rhythmic binding of CLK:BMAL1 on DNA and the transcription of its target genes, suggesting that they are regulated by as yet uncharacterized mechanisms. Here we show that rhythmic CLK:BMAL1 DNA binding promotes rhythmic chromatin opening. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

47 Samples

Download data: BW, TXT

(Submitter supplied) Over the past decade, genome-wide assays have underscored the broad sweep of circadian gene expression. A substantial fraction of the transcriptome undergoes oscillations in many organisms and tissues, which governs the many biochemical, physiological and behavioral functions under circadian control. Based predominantly on the transcription feedback loops important for core circadian timekeeping, it is commonly assumed that this widespread mRNA cycling reflects circadian transcriptional cycling. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

12 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Over the past decade, genome-wide assays have underscored the broad sweep of circadian gene expression. A substantial fraction of the transcriptome undergoes oscillations in many organisms and tissues, which governs the many biochemical, physiological and behavioral functions under circadian control. Based predominantly on the transcription feedback loops important for core circadian timekeeping, it is commonly assumed that this widespread mRNA cycling reflects circadian transcriptional cycling. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Circadian clocks are cell-autonomous oscillators regulating daily rhythms in a wide range of physiological, metabolic and behavioral processes. Conversely, metabolic signals such as redox state, NAD+/NADH and AMP/ADP ratios or heme feed back to and modulate circadian mechanisms to optimize energy utilization across the 24-hour cycle. We show that the signaling molecule carbon monoxide (CO) generated by rhythmic heme degradation is required for normal circadian rhythms as well as circadian metabolic outputs. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

8 Samples

Download data: CEL

(Submitter supplied) Genetic and molecular approaches have been critical for elucidating the mechanism of the mammalian circadian clock. Here, we demonstrate that the ClockΔ19 mutant behavioral phenotype is significantly modified by mouse strain genetic background. We map a suppressor of the ClockΔ19 mutation to a ∼900 kb interval on mouse chromosome 1 and identify the transcription factor, Usf1, as the responsible gene. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14602

13 Samples

Download data: BW

(Submitter supplied) Liver clock regulates transcription of hepatic genes in response to feeding. To explore the possibility that the microbiome influences this process, we measured the liver transcriptome in normal mice (Specific Pathogen Free or SPF mice) and compared it to the transcriptome in mice lacking microbiota (Germ Free or GF mice) at different time points over 24h. We used microarrays to detail the global programme of gene expression in liver of GF and SPF 10-12 weeks-old male C57Bl/6 male mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

40 Samples

Download data: CEL

(Submitter supplied) Mammals rely on a network of circadian clocks to control daily systemic metabolism and physiology. The central pacemaker in the suprachiasmatic nucleus (SCN) is considered hierarchically dominant over peripheral clocks, whose degree of independence, or tissue-level autonomy, has never been ascertained in vivo. Using arrhythmic Bmal1-null mice, we generated animals with reconstituted circadian expression of BMAL1 exclusively in the liver (Liver-RE). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

18 Samples

Download data: BW

(Submitter supplied) The mammalian circadian clock system is made up of individual cell and tissue clocks that function as a coherent network, however it remains unclear which rhythmic functions of the liver clock are autonomous or rely on clocks in other tissues. Here, using mice which only have a functioning liver clock, we investigate the autonomous vs non-autonomous reatures of the liver clock and diurnal rhythmicity in the liver

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

54 Samples

Download data: TSV

(Submitter supplied) Circadian clocks drive 24-h rhythms of physiology and behavior. The circadian clock of hepatocytes has been shown to regulate glucose metabolism, and we were interested if rescuing liver clock function can reverse metabolic impairments in hyperphagic/obese Clock-D19 mutant mice. We compared transcripomte regulation in livers (at Zeitgeber time ZT10) of wild-type (C57BL/6J) and Clock-D19 mice and Clock-D19 mice with genetic rescue of liver clock function using hydrodynamic tail vein injection of a WT-CLOCK expression plasmid

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

9 Samples

Download data: CEL

(Submitter supplied) Steroid Receptor 2 (SRC-2) is a coactivator involved in hepatic metabolism. To better understand its temporal involvement in metabolism genome wide profiling was performed at 2 time ZT4 and ZT18 as well as in the SRC-2 knockout mouse.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: BW

(Submitter supplied) In this study we employed unbiased, genome-wide techniques to investigate how obesity impacts BMAL1 occupancy in omental preadipocytes (OPAs) from non-obese and obese patients. Obesity relocalized BMAL1 occupancy genome-wide in omental preadipocytes. Several thousand BMAL1 binding sites were identified, some of which could be involved in pathological processes.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

7 Samples

Download data: BW

(Submitter supplied) Diet-induced obesity (DIO) is rapidly becoming a global health problem, particularly as Westernization of emerging nations continues. Currently, one third of adult Americans are considered obese and, if current trends continue, >90% of US citizens are predicted to be affected by 2050. However, efforts to fight this epidemic have not yet produced sound solutions for prevention or treatment. Our studies reveal a balanced and chronobiological relationship between food consumption, daily variation in gut microbial evenness and function, basomedial hypothalamic circadian clock (CC) gene expression, and key hepatic metabolic regulatory networks , including CC and nuclear receptors (NR), that is are essential for metabolic homeostasis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

8 Samples

Download data: CEL

(Submitter supplied) This study is a follow-up to GSE35790. This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL17021 GPL6246 GPL9185

59 Samples

Download data: BW, CEL, TXT

(Submitter supplied) The hypothesis that the oleanolic acid of olive oil might influence hepatic gene expression in an apoE was tested in mice. Gene expression was analyzed using DNA microarrays in male apoE-deficient mice that received 10 mg/kg/day of oleanolic acid for 11 weeks.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8321

2 Samples

Download data: CEL