Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circadian regulation in rat Lung

ABSTRACT: Circadian rhythms are oscillations with a periodicity of 24 hours that are controlled by an endogenous clock and are observed in virtually all aspects of mammalian function from expression of genes to complex physiological processes. The master clock is present in the suprachiasmatic nucleus (SCN) in the anterior part of the hypothalamus and controls peripheral clocks present in other parts of the body . Although much is known about the mechanism of the central clock in the SCN, the regulation of clocks present in peripheral tissues is still unclear. This study is designed to examine fluctuations in gene expression in lungs within the 24 hour circadian cycle in normal animals. The objectives of this study is to identify and analyze circadian oscillation in gene expression in lungs, and to identify the role of circadian regulation in coordinating the functioning of this dynamic organ. Fifty-four male normal Wistar rats (250-350 g body weight) were housed in a strictly controlled stress free environment with light:dark cycles of 12 hr:12hr. Three animals were sacrificed at each of 18 selected time points within the 24 hour cycle. RNA was prepared from lungs for gene arrays. Time point designations reflect time after lights on in hours.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Siddharth Sukumaran

PROVIDER: E-GEOD-25612 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Circadian regulation in rat Lung

2010-12-20 | GSE25612 | GEO

Circadian regulation in rat abdominal adipose tissue

2010-03-09 | GSE20635 | GEO

Circadian regulation in rat abdominal adipose tissue

Project description:Circadian rhythms are oscillations with a periodicity of 24 hours that are controlled by an endogenous clock and are observed in virtually all aspects of mammalian function from expression of genes to complex physiological processes. The master clock is present in the suprachiasmatic nucleus (SCN) in the anterior part of the hypothalamus and controls peripheral clocks present in other parts of the body. Although much is known about the mechanism of the central clock in the SCN, the regulation of clocks present in peripheral tissues is still unclear. This study is designed to examine fluctuations in gene expression in abdominal white adipose tissue within the 24 hour circadian cycle in normal animals. The objectives of this study is to identify and analyze circadian oscillation in gene expression in white adipose tissue, and to identify the role of circadian regulation in coordinating the functioning of this dynamic tissue. Fifty-four male normal Wistar rats (250-350 g body weight) were housed in a strictly controlled stress free environment with light:dark cycles of 12 hr:12hr. Three animals were sacrificed at each of 18 selected time points within the 24 hour cycle. RNA was prepared from abdominal adipose tissue for gene arrays. Two samples were not used due to RNA degradation: Adipose .25-1 and Adipose 11-2. Time point designations reflect time after lights on in hours.

2010-03-09 | E-GEOD-20635 | biostudies-arrayexpress

Circadian behavior is light-reprogrammed by plastic DNA methylation

Project description:The timing of daily “circadian” behavior can be highly variable among different individuals, and twin studies suggest that about half of this variability is environmentally controlled. Similar plasticity can be seen in mice exposed to an altered lighting environment – for example, 22-hour days instead of 24-hour ones – which stably alters the genetically determined period of circadian behavior for months. The mechanisms mediating these environmental influences are unknown. Here, we show that transient exposure of mice to such lighting stably alters global transcription in the suprachiasmatic nucleus of the hypothalamus (the SCN, the “master clock” tissue determining circadian behavior in mammals). We have also showed that, these changes in transcription are due to change in DNA methylation in the SCN. Indeed, genome-wide methylation profiling revealed global alterations in promoter DNA methylation in the SCN. Importantly, infusion of a methyltransferase inhibitor to the SCN during 22-hour days suppressed period changes. We also found that these behavioral and DNA methylation changes are reversible upon entrainment to 24-hours days. We conclude that the SCN utilizes DNA methylation as a mechanism to drive circadian clock plasticity. MeDIP array of profiling, demonstrated that genomicDNA methylation changes in mice entrained to short-T cycle.

2014-01-14 | GSE54021 | GEO

Comprehensive and cell-type-based analysis of microRNA profiles and functions in mouse suprachiasmatic nucleus

Project description:Circadian rhythm governs a variety of biological processes in essentially all living organisms and microRNAs have been found to play important roles in the post-transcriptional regulation of circadian clocks. However, the microRNA expression profile in mouse central circadian clock – suprachiasmatic nucleus (SCN) is lacking. In this study, we systematically profiled microRNAs in mouse SCN and SCN subtype neurons by high sensitive small RNA sequencing and examined their potential circadian functions. We found that a large fraction of known microRNAs are SCN-specific and 20 of them are also oscillated significantly. Predicted targets of these 20 microRNAs were enriched in circadian rhythm pathway as well. Integrated analysis of microRNA and mRNA revealed 3 clock-related functional modules, demonstrating the regulation roles of miR-24, miR-30, miR-7a, miR-7b, miR125a and miR125b in SCN. Furthermore, we observed distinct microRNA profiles in SCN subtype neurons with divergent regulatory functions, which correlated with their differential spatial distribution. In addition, we also identified a proportion of light-response microRNAs in SCN, one of which was miR-7a. Further experiments showed that miR-7a directly target fos and regulated its translation in SCN. All these observations indicate important circadian regulation roles of microRNA in central circadian clock.

2021-08-18 | GSE133051 | GEO

Circadian regulation of gene expression in the SCN (gene expression)

Project description:We performed a circadian RNA expression profile of the mammalian biological clock, the suprachiasmatic nucleus (SCN) in C57/BL6 mice, at 2-hour resolution using microarrays, and at 6-hour resolution using RNA-seq. 24 samples total covering 24 time points, with no replicates. SCN samples from mouse brains collected every 2 hours for 2 days (24 samples total).

2015-12-31 | E-GEOD-70384 | biostudies-arrayexpress

Circadian key component CLOCK/BMAL1 interferes with segmentation clock in mouse embryonic organoids

Project description:In mammals, circadian clocks are strictly suppressed during early embryonic stages as well as pluripotent stem cells, by the lack of CLOCK/BMAL1 mediated circadian feedback loops. During ontogenesis, the innate circadian clocks emerge gradually at a late developmental stage, then, with which the circadian temporal order is invested in each cell level throughout a body. Meanwhile, in the early developmental stage, a segmented body plan is essential for an intact developmental process and somitogenesis is controlled by another cell-autonomous oscillator, the segmentation clock, in the posterior presomitic mesoderm (PSM). In the present study, focusing upon the interaction between circadian key components and the segmentation clock, we investigated the effect of the CLOCK/BMAL1 on the segmentation clock Hes7 oscillation, revealing that the expression of functional CLOCK/BMAL1 severely interferes with the ultradian rhythm of segmentation clock in induced PSM and gastruloids. RNA sequencing analysis showed that the premature expression of CLOCK/BMAL1 affects the Hes7 transcription and its regulatory pathways. These results suggest that the suppression of CLOCK/BMAL1-mediated transcriptional regulation during the somitogenesis may be inevitable for intact mammalian development.

2021-12-09 | GSE181295 | GEO

Diurnal cycle effect on whole leaf, mesophyll and vasculature: time course

Project description:Many organisms acquired circadian clock system to adapt daily and seasonal environmental changes. Mammals have the master clock in the brains’ suprachiasmatic nucleus (SCN) that synchronizes other circadian clocks in the peripheral tissues or organs. Plants also have circadian clock in their bodies, but the presence of the tissue-specific functions of circadian clock is remained elusive. The aim of this experiment is to compare tissue-specific gene expression profile using gene expression Microarray.

2014-09-10 | GSE50438 | GEO

Twenty-four hour rhythms in the absence of the clock gene Bmal1

Project description:Circadian (~24 hour) clocks exist in almost all types of living organism and play a fundamental role in regulating daily physiological and behavioural processes. The transcription factor BMAL1 (ARNTL) is thought to be one of the principal drivers of the molecular clock in mammals since its deletion abolishes 24-hour activity patterning, an important physiological output of the clockwork. However, whether or not Bmal1-/- mice can nevertheless display molecular 24-hour rhythms is unknown. Here, we determined whether Bmal1 function is necessary for daily molecular oscillations in two tissues – skin fibroblasts and liver. Unexpectedly, both tissues exhibited robust 24-hour oscillations over 2-3 days in the absence of any exogenous synchronizers such as daily light or temperature cycles. This demonstrates a competent 24-hour molecular pacemaker in Bmal1 knockouts. Indeed, molecular oscillations were pervasive throughout the transcriptome, proteome and phosphoproteome of Bmal1-/- mice. In particular, several proteins exhibited rhythmic phosphorylation in both Bmal1-proficient and -deficient cells, highlighting an unanticipated role for post-translational regulators in 24-hour rhythms in the absence of any known clock mechanisms.

2020-02-17 | PXD009243 | Pride

Transcription profiling of mouse liver cells with a conditionally active liver clock to descriminate between rhythmic gene expression driven by cyclic systemic cues and local oscillators

Project description:The mammalian circadian timing system consists of a master pacemaker in the suprachiasmatic nucleus (SCN) that synchronizes self-sustained oscillators in most peripheral cells. Rhythmic gene expression in peripheral tissues can be driven by cyclic systemic cues emanating from the SCN or by local oscillators. To discriminate between these two mechanisms, we engineered a mouse strain with a conditionally active liver clock. Transcriptome profiling revealed that the circadian transcription of most genes depends on functional hepatocyte clocks. However, the expression of 31 genes, including mPer2, oscillates robustly in clock-arrested hepatocytes. Such genes may be implicated in the synchronization of liver oscillators

2006-12-30 | E-MEXP-842 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data