GEO DataSets

(Submitter supplied) We molecularly characterized thousands of liver hepatocytes cells at different time points around the circadian clock. This enable us to reconstruct mRNA expression profiles in space and time.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

10 Samples

Download data: TXT

(Submitter supplied) Mammalian gene expression displays widespread circadian oscillations. Rhythmic transcription underlies the core clock mechanism, but it cannot explain numerous observations made at the level of protein rhythmicity. We have used ribosome profiling in mouse liver to measure the translation of mRNAs into protein around-the-clock and at high temporal and nucleotide resolution. Transcriptome-wide, we discovered extensive rhythms in ribosome occupancy, and identified a core set of ≈150 mRNAs subject to particularly robust daily changes in translation efficiency. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

48 Samples

Download data: TXT

(Submitter supplied) Virtually every mammalian tissue exhibits rhythmic expression in thousands of genes, which activate tissue-specific processes at appropriate times of the day. Much of this rhythmic expression is thought to be driven cell-autonomously by molecular circadian clocks present throughout the body. However, increasing evidence suggests that systemic signals, and more specifically rhythmic food intake (RFI), can regulate rhythmic gene expression independently of the circadian clock. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

72 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

120 Samples

Download data

(Submitter supplied) The circadian clock and rhythmic food intake are both important regulators of rhythmic gene expression in the liver. It remains, however, elusive to which extent the circadian clock network and natural feeding rhythms contribute to rhythmic gene expression. To systematically address this question, we developed an algorithm to investigate differential rhythmicity between a varying number of conditions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

96 Samples

Download data: TXT

(Submitter supplied) The circadian clock and rhythmic food intake are both important regulators of rhythmic gene expression in the liver. It remains, however, elusive to which extent the circadian clock network and natural feeding rhythms contribute to rhythmic gene expression. To systematically address this question, we developed an algorithm to investigate differential rhythmicity between a varying number of conditions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

24 Samples

Download data: TXT

(Submitter supplied) The mammalian liver is composed of repeating hexagonal units termed lobules. Spatially-resolved single-cell transcriptomics revealed that about half of hepatocyte genes are differentially expressed across the lobule. Technical limitations impede reconstructing similar global spatial maps of other hepatocyte features. Here, we used zonated surface markers to sort hepatocytes from defined lobule zones with high spatial resolution. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL21265

24 Samples

Download data: TXT, XLSX

(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

(Submitter supplied) Using chromatin immuno-precipitation (ChIP) combined with deep sequencing (ChIP-seq) we obtained a time resolved and genome-wide map of BMAL1 binding in mouse liver, which allowed to identify over two thousand binding sites with peak binding narrowly centered around Zeitgeber time (ZT) 6. Annotation of BMAL1 targets confirms carbohydrate and lipid metabolism as the major output of the circadian clock in mouse liver. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

13 Samples

Download data: BEDGRAPH

(Submitter supplied) To systematically understand how the circadian clock and the nutrient-driven rhythm integrate to regulate SREBP1 activity, we evaluated genome-wide the binding of SREBP1 to its targets along the day in wild-type (WT) C57BL/6mice. The recruitment of SREBP1 to the DNA showed a highly circadian behaviour, with a maximum during the fed status. However, the temporal expression of SREBP1 targets was not always synchronized with its binding. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

18 Samples

Download data: BEDGRAPH

(Submitter supplied) The circadian clock is an evolutionarily conserved mechanism that drives rhythmic expression of downstream genes. The core circadian clock drives the expression of clock-controlled genes either directly or indirectly, which in turn play critical roles in carrying out many rhythmic physiological processes. Nevertheless, the molecular mechanisms by which clock output genes orchestrate rhythmic signals from the brain to peripheral tissues are largely unknown. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21306

96 Samples

Download data: TXT

(Submitter supplied) The oscillation status of the circadian clock during late gestation is not clear. To gain a better understanding on the oscillation state of the clock and possible influences by maternal cues, we performed transcriptome analyses on the fetal liver tissue during late gestation. Fetal liver transcriptome data were analyzed and compared to adult mouse data in the public database: GSE11923 and GSE13093 (only samples GSM327130 to GSM327141). more...

Organism:

Mus musculus

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL8321

24 Samples

Download data: CEL, TXT

(Submitter supplied) Circadian transcriptional rhythms are necessary for lipid metabolic homeostasis. Disruptions can lead to metabolic diseases. Whether epigenetic N6-methyladenosine (m6A) mRNA methylation impacts circadian regulation of lipid metabolism is unclear. Here, we show m6A mRNA methylation oscillations in murine liver depend upon a functional circadian clock. Hepatic deletion of Bmal1 increased m6A mRNA methylation, particularly of PPaRα. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

12 Samples

Download data: TXT

(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:

GPL9185 GPL17021 GPL6246

59 Samples

Download data: BW, CEL, TXT

(Submitter supplied) In the chronobiology field, a fundamental dichotomy exists to explain daily rhythmicity of biological processes: these can be elicited in response to cyclic extrinsic/environmental signals such as light, or driven endogenously by the circadian clock. In mammals, the circadian clock ticks in almost every cell of the body, and functions based on a network of transcription-translation feedback loops. The PI3K-AKT signaling pathway relays environmental information of nutritional/metabolic state to regulate cell size and proliferation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

140 Samples

Download data: XLSX

(Submitter supplied) Hepatic gene expression was examined every 3 hours for 24 hours following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure on the circadian rhythmicity of hepatic gene expression in C57BL/6 male mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

48 Samples

Download data: TXT

(Submitter supplied) Aryl hydrocarbon receptor ChIP-Seq performed in livers of male mice gavaged with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) for 2hrs

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

10 Samples

Download data: BIGWIG

(Submitter supplied) Circadian profiling of total RNA collected from wildtype and dnClk adult Drosophila fatbody

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

36 Samples

Download data: CEL

(Submitter supplied) Introduction: A considerable proportion of mammalian gene expression undergoes circadian oscillations. Post-transcriptional mechanisms likely make important contributions to mRNA abundance rhythms. Aim: We have investigated how microRNAs contribute to core clock and clock-controlled gene expression using mice in which microRNA biogenesis can be inactivated in the liver. Results: While the hepatic core clock was surprisingly resilient to microRNA loss, whole transcriptome sequencing uncovered widespread effects on clock ouput gene expression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

24 Samples

Download data: GTF, RPKM

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL16570

30 Samples

Download data: BIGWIG, CEL