GEO DataSets

(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) Investigation of diurnal gene expression in liver over the course of 2 days at 4hr interval.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL22527

12 Samples

Download data: NCD, PAIR, TXT

(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) Plasticity in the daily timing of activity has been observed in a wide variety of species, yet the underlying mechanisms driving nocturnality and diurnality remain to be discovered. By regulating how much wheel-running activity will be rewarded with a food pellet, we can manipulate energy balance, and switch mice to be nocturnal or diurnal. Here we present the rhythmic transcriptome of 21 tissues, including 17 brain regions (hypothalamic, thalamic, cortical), sampled every 4 hours over a 24-hour period from nocturnal and diurnal male CBA/CaJ mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

493 Samples

Download data: CSV

(Submitter supplied) The human striatum can be subdivided into the caudate, putamen, and nucleus accumbens (NAc). Each of these structures have some overlapping and some distinct functions related to motor control, cognitive processing, motivation, and reward. Previously, we used a “time of death” approach to identify diurnal rhythms in RNA transcripts in human cortical regions. Here, we identify molecular rhythms across the three striatal subregions collected from postmortem human brain tissue in subjects without psychiatric or neurological disorders. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

177 Samples

Download data: CSV

(Submitter supplied) The circadian clock enables organisms to rapidly adapt to the ever-changing environmental conditions that are caused by daily light/dark cycles. Circadian clock genes universally affect key agricultural traits, particularly flowering time. Here, we show that OsPRR37, a circadian clock gene, delays rice flowering time in an expression level-dependent manner. Using high-throughput mRNA sequencing on an OsPRR37 overexpressing transgenic line (OsPRR37-OE5) and the recipient parent Guangluai4 that contains the loss-of-function Osprr37, we identify 14,992 genes that display diurnal rhythms, which account for 52.9% of the transcriptome. more...

Organism:

Oryza sativa Indica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21027

36 Samples

Download data: XLS

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

Organism:

Mus musculus

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL6246

384 Samples

Download data: CEL, TAB

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

96 Samples

Download data: TAB, TXT

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

288 Samples

Download data: CEL

(Submitter supplied) Altered daily patterns of hormone action are suspected to contribute to metabolic disease. It is poorly understood how the adrenal glucocorticoid hormones contribute to the coordination of daily global patterns of transcription and metabolism. Here, we examined diurnal metabolite and transcriptome patterns in a zebrafish glucocorticoid deficiency model by RNA-Seq, NMR spectroscopy and liquid chromatography-based methods. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16509 GPL15583

20 Samples

Download data: TXT

(Submitter supplied) Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. more...

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24468

6 Samples

Download data: BW

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

Organism:

Oryza sativa

Type:

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

Platform:

GPL24468

154 Samples

Download data: BW, TXT

(Submitter supplied) Genome-wide rhythmic occupancy of RNA polymerase II (RNAPII) is highly coordinated with rhythmic genes expression. Rhythmic RNAPII binding dynamically modulates diurnal 3D genome architecture remodeling with 91% of the chromatin interactions were altered. The rhythmic genes cluster at the 8:00 (AM) circadian phase form spatial interacting clusters in turn assist coordinated rhythmic gene expression, while non-rhythmic genes tend to tether together and contribute to expression at 20:00 (PM) circadian window. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24468

12 Samples

Download data: BW

(Submitter supplied) Genome-wide rhythmic occupancy of RNA polymerase II (RNAPII) is highly coordinated with rhythmic genes expression. Rhythmic RNAPII binding dynamically modulates diurnal 3D genome architecture remodeling with 91% of the chromatin interactions were altered. The rhythmic genes cluster at the 8:00 (AM) circadian phase form spatial interacting clusters in turn assist coordinated rhythmic gene expression, while non-rhythmic genes tend to tether together and contribute to expression at 20:00 (PM) circadian window. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24468

2 Samples

Download data: BW

(Submitter supplied) Genome-wide rhythmic occupancy of RNA polymerase II (RNAPII) is highly coordinated with rhythmic genes expression. Rhythmic RNAPII binding dynamically modulates diurnal 3D genome architecture remodeling with 91% of the chromatin interactions were altered. The rhythmic genes cluster at the 8:00 (AM) circadian phase form spatial interacting clusters in turn assist coordinated rhythmic gene expression, while non-rhythmic genes tend to tether together and contribute to expression at 20:00 (PM) circadian window. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24468

20 Samples

Download data: BEDPE

(Submitter supplied) Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24468

98 Samples

Download data: BW

(Submitter supplied) Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24468

16 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) 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