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

Urinary bladder in constant darkness: time course

ABSTRACT: Analysis of urinary bladder in wild-type C57BL/6 females sacrificed every 4 hours at six time points under constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions. Results provide insight into circadian gene expression patterns in normal urinary bladder. Analysis of urinary bladder in wild-type C57BL/6 females sacrificed every 4 hours at six time points (n=2 for each time (CT 0, 4, 8, 12 and 20)) under constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions.

ORGANISM(S): Mus musculus

SUBMITTER: Hiromitsu Negoro

PROVIDER: E-GEOD-35795 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Effects of extensive fasting and subsequent feeding on hepatic transcription

Project description:Temporally restricted feeding has a profound effect on the circadian clock. Fasting and feeding paradigms are known to influence hepatic transcription. This dataset shows the dynamic effects of refeeding mice after a 24hour fasting period. Mice were entrained for two weeks under ad libitum access to food. Mice were then released into constant darkness and food was withdrawn at CT4 on the first day in constant darkness. On the second day in constant darkness mice were either fed (Refed) or continously fasted (Fast) at CT4. Liver tissue was collected at the indicated timepoints. Total RNA was extracted and standard Affymetrix protocol were used for amplification, labeling and hybridization

2009-11-23 | E-GEOD-13063 | biostudies-arrayexpress

Transcription profiling time series of Rattus norvegicus SCN2.2 cell line and in vivo suprachiasmatic nucleus samples to compare oscillatory properties of each transcriptome

Project description:To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. This SuperSeries is composed of the following subset Series:; GSE1654: Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells (3 biological replicates); GSE1673: Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells: Comparison to Long-Evans Rat SCN Experiment Overall Design: Refer to individual Series

2007-10-10 | E-GEOD-4192 | biostudies-arrayexpress

RNA-seq of Mus musculus to investigate the role of RNA editing for the gene expression in the suprachiasmatic nuclei of the hypothalamus

Project description:RNA editing is essential for the formation of functional properties of ionotropic glutamate channels. Previously, we demonstrated the regulation of RNA editing upon manipulation with neural activity in vitro. The hypothalamic suprachiasmatic nuclei (SCN), which serve as a master circadian pacemaker depends on glutamatergic neurotransmission, in particular for signal transmission from the retina, and they exhibit spontaneous 24h rhythmical neural activity. We observed changes in the extent of ionotropic glutamate receptor RNA editing in the SCN during the 24h cycle. Therefore, we aimed to understand the overall role of RNA editing for the mechanism of SCN function and to evaluate the impact of RNA under editing on gene expression.

2023-06-29 | E-MTAB-11408 | biostudies-arrayexpress

Genome-wide analysis of toc1-2 transcriptional networks

Project description:To gain insights into the mechanisms of TOC1 function in the Arabidopsis circadian clock we performed transcriptional profiling of Wild-Type (WT) and and TOC1 mutant plants (toc1-2) under constant light conditions for two days. Comparisons of WT and toc1-2. Two biological replicates each per array. Two Arabidopsis Oligonucleotide Microarrays (two-color Cy3 and Cy5). synchronized under 12-hour light:12-hour dark (LD) cycles for 10 days followed by two days under constant light conditions. Samples were collected at circadian time 16 (CT16).

2010-05-05 | E-GEOD-18001 | biostudies-arrayexpress

Mouse SCN in LC-MSMS - The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry.

Project description:The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry.

2014-09-10 | PXD000778 | Pride

Transcription profiling of aortae from mice that have been subjected to constant darkness to study the transcriptional responses at different time points.

Project description:After 2 week acclimation to 12 hr/12 hr light/dark regimen, C57/BL6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint). Keywords = aorta, murine, circadian

2007-11-06 | E-GEOD-414 | biostudies-arrayexpress

transcriptional analysis of breast circadian clock

Project description:Circadian clocks drive ~24 hr rhythms in tissue physiology. They rely on transcriptional/translational feedback loops driven by interacting networks of clock complexes.To gain insights into the role of the mammary clock, circadian time-series microarrays were performed to identify rhythmic genes in vivo. Breast tissues were isolated at 4 hr intervals for two circadian (24 hourly) cycles, from mice kept under constant darkness to avoid any light- or dark-driven genes.

2017-12-01 | E-MTAB-5330 | biostudies-arrayexpress

Time-of-day-dependent light-induction of gene expression in the chicken pineal gland

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

Genome-wide screen reveals rhythmic regulation of genes involved in odor processing in the olfactory epithelium

Project description:Odor discrimination behavior displays circadian fluctuations in mice indicating that mammalian olfactory function is under control of the circadian system. This is further supported by the facts that odor discrimination rhythms depend on the presence of clock genes and that olfactory tissues contain autonomous circadian clocks. However, the molecular link between circadian function and olfactory processing is still unknown. In order to elucidate the molecular mechanisms underlying this link, we focused on the olfactory epithelium (OE), the primary target of odors and the site of the initial events in olfactory processing. We asked whether olfactory sensory neurons (OSNs) within the OE possess an autonomous circadian clock and whether olfactory pathways are under circadian control. Employing clock gene-driven bioluminescence reporter assays, immunohistochemistry and a time-dependent microarray-based transcriptome analysis on OE samples, we found robust circadian rhythms of core clock genes and their proteins in OSNs, suggesting that the OE indeed contains an autonomous circadian clock. Furthermore, we identified several OSN-specific components of the olfactory pathway that are under circadian control, including several candidates with putative roles in circadian olfactory processing, such as KIRREL2 -- an established factor involved in short-term OSN activation. The spatiotemporal expression patterns of our candidate proteins suggest that they are involved in short-term anabolic processes to rhythmically prepare the cell for peak performances and to promote circadian function of OSNs. We performed a genome-wide expression study with RNA from OE tissue extracted at 4-h intervals in constant darkness from previously entrained mice. Total RNA of four mice per sampling time was pooled in equal amounts.

2015-11-04 | E-GEOD-69853 | biostudies-arrayexpress

circadian clock in cartilage

Project description:This experiment investigated the circadian clock in mice cartilage. A microarray time-series was performed using xiphoid tissue (metasternum) from mice in constant darkness. Time points were every 4 hr for 40 hr in total.

2013-10-19 | E-MEXP-3780 | 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