GEO DataSets

(Submitter supplied) BACKGROUND: The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We have used ribosome profiling to explore the contribution of translation efficiency to temporal gene expression in kidney, and contrasted our findings with liver data available from the same mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17021

48 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) Physiological and behavioral circadian rhythms are driven by a conserved transcriptional/translational negative feedback loop in mammals. Although most core clock factors are transcription factors, post-transcriptional control introduces delays that are critical for circadian oscillations. Little work has been done on circadian regulation of translation, so to address this deficit we conducted ribosome profiling experiments in a human cell model for an autonomous clock. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

96 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

96 Samples

Download data: CEL

(Submitter supplied) Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

36 Samples

Download data: CEL

(Submitter supplied) Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

36 Samples

Download data: CEL

(Submitter supplied) Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL

(Submitter supplied) Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL

(Submitter supplied) Diurnal (i.e., 24-hour) physiological rhythms depend on transcriptional programs controlled by a set of circadian clock genes/proteins. Systemic factors like humoral and neuronal signals, oscillations in body temperature, and food intake align physiological circadian rhythms with external time. Thyroid hormones (THs) are major regulators of circadian clock target processes such as energy metabolism, but little is known about how fluctuations in TH levels affect the circadian coordination of tissue physiology. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23038

70 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17021

168 Samples

Download data: TXT

(Submitter supplied) Diurnal oscillations of gene expression are a hallmark of rhythmic physiology across most living organisms. Such oscillations are controlled by the interplay between the circadian clock and feeding rhythms. While rhythmic mRNA accumulation has been extensively studied, comparatively less is known about their transcription and translation. Here, we quantified simultaneously temporal transcription, accumulation, and translation of mouse liver mRNAs under physiological light-dark conditions and ad libitum or night-restricted feeding in wild-type and Bmal1 deficient animals. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

84 Samples

Download data

(Submitter supplied) Diurnal oscillations of gene expression are a hallmark of rhythmic physiology across most living organisms. Such oscillations are controlled by the interplay between the circadian clock and feeding rhythms. While rhythmic mRNA accumulation has been extensively studied, comparatively less is known about their transcription and translation. Here, we quantified simultaneously temporal transcription, accumulation, and translation of mouse liver mRNAs under physiological light-dark conditions and ad libitum or night-restricted feeding in wild-type and Bmal1 deficient animals. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

84 Samples

Download data

(Submitter supplied) Evolutionary conserved biological rhythms play a fundamental role in the physiology and behavior of all light-sensitive organisms. Generation of rhythmic expression of clock-controlled genes is orchestrated by a molecular circadian clock constitutes by interconnected negative feedback loops of transcription factors. In this study, we want to characterize gene which also present a rhythmic translation through the characterization of genes with a rhythmic polysomal/total RNA ratio.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

48 Samples

Download data: CEL, CHP

(Submitter supplied) Temporal control of physiology requires the interplay between gene networks involved in daily timekeeping and tissue function across different organs. How the circadian clock interweaves with tissue-specific transcriptional programs is poorly understood. Here we dissected temporal and tissue-specific regulation at multiple layers of gene regulation by examining mouse tissues with an intact or disrupted clock over time. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13112 GPL17021

44 Samples

Download data: TXT

(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) Male KO (Syt10-Cre/Cre x Bmal1-flox/-) and CON (Syt10-Cre/Cre x Bmal1-+/-) mice were entrained to 12h:12h light:dark conditions for two weeks and sacrificed at 4 different time points (CT1, 7, 13, 19) on the second day after release into constant darkness conditions. Total RNA was isolated from epididymal white adipose tissue biopsies and subjected to microarray hybridization.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

24 Samples

Download data: CEL

(Submitter supplied) Spatio-temporal gene expression patterns underlie time-of-the day specific functional specialization of different organs. Although circadian gene expression atlases from model organisms including the nocturnal mouse are available, they are limited to a few peripheral organs. Here we report the circadian transcriptome of 64 different tissues, including 22 different brain regions, sampled every 2 h over 24 h, from the diurnal primate Papio Anubis. more...

Organism:

Papio anubis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23487

767 Samples

Download data: CSV

(Submitter supplied) Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and post transcriptional mechanisms are considered important to drive rhythmic RNA expression, however, the extent to which each regulatory process contributes to the rhythmic RNA expression remains controversial. To systematically address this, we monitored RNA dynamics using metabolic RNA labeling technology during a circadian cycle in mouse fibroblasts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21103

48 Samples

Download data: CSV

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

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL30082 GPL20660

160 Samples

Download data: TXT

(Submitter supplied) We report the genome-wide impact of rhythmic P-eIF2α levels in vivo by performing ribosome profiling and RNA-seq in Neurospora crassa samples grown over a circadian time course. We identified candidate genes which showed rhyhmic ribosome occupancy in WT cells but lost rhythms in mRNA levels and ribosome occupancy in the clock mutant Dfrq, eIF2α kinase knockout Dcpc-3, and constitutively active kinase mutant cpc-3c cells. more...

Organism:

Neurospora crassa

Type:

Other

Platforms:

GPL20660 GPL30082

80 Samples

Download data: TXT