E-GEOD-46621
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA201242PRJNA188075PRJNA202212
PROVIDER: E-GEOD-46621 | ExpressionAtlas | 2014-07-03
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:Light pulses at the end of the day or night be able to control the phase of the circadian clock. Pulses in the middle of the night has not effect on the circadian oscilations. To understand how the circadian clock gate the light signal in the middle of the night we used microarrays to characterize the light effect in the whole expression profile. Plants of Arabidopsis thalina (Columbia ecotype) were grown in 12/12 light/dark cicles for 15 days and then were tranfer to continuous dark . Plants were slplit in two groups. First group recieved 1hr light pulse in the middle of the night (Night treatment), second group recieve 1hr light pulse in the middle of the subjective day (Day Treatment). Samples of both groups were collected without light pulse named as a control.
2013-08-02 | E-GEOD-46621 | biostudies-arrayexpress
Project description:Light pulses at the end of the day or night be able to control the phase of the circadian clock. Pulses in the middle of the night has not effect on the circadian oscilations. To understand how the circadian clock gate the light signal in the middle of the night we used microarrays to characterize the light effect in the whole expression profile.
2013-08-02 | GSE46621 | GEO
Project description:Many hypoxia related diseases present a time of day dependency. Here, we examine the difference in transcriptional response to hypoxia (4h, 6% O2), in different times of day, namely the middle of the light phase and the middle of the dark phase. Additionally, many rhythmic processes in mammals are controlled by the circadian clock. to examine the dependency of the hypoxic response on the molecular circadian clock, we repeated the experiment under constant darkness regimen with either wild type mice or Per1,2 double knock out mice (which lack a functional clock), and sequenced the liver transcriptome.
2019-12-08 | GSE130613 | GEO
Project description:In most organisms biological processes are partitioned, or phased to specific times over the day through interactions between external cycles of temperature (thermocycles) and light (photocycles), and the endogenous circadian clock. This orchestration of biological activities is achieved in part through an underlying transcriptional network. To understand how thermocycles, photocycles and the circadian clock interact to control time of day specific transcript abundance in Arabidopsis thaliana, we conducted four diurnal and three circadian two-day time courses using Affymetrix GeneChips (ATH1). All time courses were carried out with seven-day-old seedlings grown on agar plates under thermocycles (HC, hot/cold) and/or photocycles (LD, light/dark), or continuous conditions (LL, continuous light; DD, continuous dark, HH, continuous hot). Whole seedlings (50-100), including roots, stems and leaves were collected every four hours and frozen in liquid nitrogen. The four time courses interrogating the interaction between thermocycles, photocycles and the circadian clock were carried out as two four-day time courses. Four-day time courses were divided into two days under diurnal conditions, and two days under circadian conditions of continuous light and temperature. Thermocycles of 12 hours at 22C (hot) and 12 hours at 12C (cold) were used in this study. The two time courses interrogating photoperiod were conducted under short days (8 hrs light and 16 hrs dark) or long days (16 hrs light and 8 hrs dark) under constant temperature. In addition, the photoperiod time courses were in the Landsberg erecta (ler) accession, in contrast to the other time courses that are in the Columbia (col) background. The final time course interrogated circadian rhythmicity in seedlings grown completely in the dark (etiolated). Dark grown seedlings were synchronized with thermocycles, and plants were sampled under the circadian conditions of continuous dark and temperature.
2008-01-18 | E-MEXP-1304 | biostudies-arrayexpress
Project description:The objectives of this study was to understand the implication of early (day 1:ZT8) vs late (day 8 [for female]/day 9 [for males]:ZT176/200) reentrainment in mouse pancreas following a chronic (1-month) phase shift protocol. 4-6 week old mice underwent 4 weeks of either a normal circadian light-dark cycle or a circadian disrupted light-dark cycle whereby mice were phase shifted forward 8 hours every 2-3 days. At 4 weeks all mice were normalized to normal circadian conditions 12 hours prior to the 4 week mark. Mice were then sacraficed at 14:00 each day. Of the mice evaluated, those from ZT8 and ZT176/200 were selected for further evaluation with RNA-sequencing.
2021-01-21 | GSE165199 | GEO
Project description:Compared analysis of the transcriptomes of 12-day old seedlings from wild type Col-0 treated with NO for 15, 30 and 60 min vs untreated control seedlings. Samples were harvested 12 h after dawn of day 12 after sowing and seedlings were grown under long days (16 h light / 8 h darkness) photoperiodic conditions.
2015-12-01 | GSE75509 | GEO
Project description:Light has a strong effect on whole organism physiology, such as the circadian rhythms that are phase delayed and advanced by light given at early and late subjective night, respectively. Despite the importance of the phase-dependent light responses, little is known about the underlying molecular mechanism. We performed a comprehensive analysis of genes induced by light in a phase-dependent manner in the chicken pineal gland, an organ that represents a unique vertebrate clock system harboring intrinsic light sensitivity. Newborn chicks were entrained to 12-h light/12-h dark cycle for 7 days then transferred to constant darkness for a day to be exposed to light for 1 h from CT (circadian time) 6 (representing subjective day), CT14 (early subjective night) or CT22 (late subjective night). Control animals were kept in the dark without light pulse. The pineal glands were isolated at the end of the 1-h light pulse for gene expression analysis by Affymetrix GeneChip. Each condition contains 2 biological samples.
2011-03-08 | E-GEOD-21915 | biostudies-arrayexpress
Project description:It is well known that many genes are expressed in the retina where they show a clear daily pattern of expression. Although several studies have investigated gene expression in the retina, no study – so far - has investigated the daily and the circadian pattern of gene expression using microarray. In the present study we propose to investigate the daily and circadian pattern of expression in the retina. To determine gene expression in the retina in Light:Dark cycles and in constant condition (constant dim light) in the rat. We hypothesize that (a) different genes are expressed in different retinal layers and (b) the pattern of expression of the same genes can differ among the different layers. Wistar rats (3 for each time point) will be killed in the middle of the day (ZT6) and in the middle of the night (ZT18). Eyeballs will be collected and the retina will be removed and immediately frozen and then stored at -80 oC. The same experiment will be repeated on animals that have been maintained in constant dim light for 3. Retinas (3 for each time point) will be obtained from animal killed at CT6 (middle subjective day) and CT 18 (middle subjectice night) and stored at – 80 oC. The samples will be then shipped to NINDS-NIMH array facility for analysis. Keywords: time-course
2005-07-06 | GSE2868 | GEO
Project description:Purpose: Circadian clock in plants temporally coordinates biological processes throughout the day synchronizing gene expression with environmental changes. Here, we examined the genome-wide circadian and diurnal control of Arabidopsis transcriptome using high throughout RNA-seq approach. Methods: Transcriptional and posttranscritional profiles were identified and characterized for Arabidopsis seedlings grown under continuous light or long-day condition (16 h light/8 h dark) for one day (each condition has two biological replicates). Results: We show that rhythmic posttranscriptional regulation is also a significant factor for genome-wide profile of circadian plant transcriptome. Two major posttranscriptioal mechanisms alternative splicing (AS) and alternative polyadenylation (APA) show circadian rhythmicity, resulting from the oscillation in the genes invovled in AS and APA. Conclusions: Arabidopsis circadian clock not only controls the transcription of genes, but also affects their posttranscriptional regulation through regulating AS and APA.
2020-01-14 | GSE137732 | GEO
Project description:The mammalian master circadian pacemaker within the suprachiasmatic nucleus (SCN) maintains tight entrainment to the 24 hr light/dark cycle via a sophisticated clock-gated rhythm in the responsiveness of the oscillator to light. Intriguingly, entrainment is not merely a passive response, instead the internal oscillator responds and adjust its own timing to entrainment signals discriminating the time of day. For example, exposure to brief light pulses in the first and final hours of the subjective generate circadian phase delays and advances respectively; whereas similar photic pulses during the subjective day does not modify the phase. A central event in this light entrainment process appears to be the rapid induction of gene expression via the ERK/MAPK pathway. We used microarray-based expression profiling of the suprachiasmatic nucleus to examine the role of MAPK signaling in the light-evoked transcriptional response. We focused on three circadian timepoints that define the unique, clock-time delimited response properties of the SCN to light: the subjective day, early subjective night, and late subjective night.
2021-03-24 | GSE165799 | GEO