Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-throughput sequencing of mouse liver transcriptome in Clock mutant animals

ABSTRACT: Circadian profile of polyA RNA by RNA-Seq, collected from ClockΔ19 mouse liver at CT22, CT28, CT34, CT40. RNA from three livers pooled per time point.

ORGANISM(S): Mus musculus

PROVIDER: GSE41082 | GEO | 2015/08/05

SECONDARY ACCESSION(S): PRJNA175697

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

High-throughput sequencing of mouse liver transcriptome in Clock mutant animals

Project description:Circadian profile of polyA RNA by RNA-Seq, collected from Clock?19 mouse liver at CT22, CT28, CT34, CT40. RNA from three livers pooled per time point. 4 Clock mutant samples with no replicates

2015-08-05 | E-GEOD-41082 | biostudies-arrayexpress

High-throughput sequencing of mouse liver transcriptome.

Project description:Circadian profile of polyA RNA by RNA-Seq, collected from mouse liver at CT23, CT29, CT35, CT41, CT47, CT53, CT59, CT65. RNA from three livers pooled per time point.

2015-08-05 | GSE40190 | GEO

High-throughput sequencing of mouse liver transcriptome.

Project description:Circadian profile of polyA RNA by RNA-Seq, collected from mouse liver at CT23, CT29, CT35, CT41, CT47, CT53, CT59, CT65. RNA from three livers pooled per time point. 8 wildtype samples with no replicates.

2015-08-05 | E-GEOD-40190 | biostudies-arrayexpress

Clock rescue in the brain restores 12- and 24- hour rhythms in the liver

Project description:Circadian profiling was performed in mouse livers from three different genotypes/treatments: Wildtype, Clock mutant, and brain-specific Clock rescue. Rescuing Clock specifically in the brain partially rescued robust circadian and harmonic rhythms. Samples were collected every 2 hours for 48 hours from 2-4 mice per time point; samples were pooled and analyzed using Affymetrix Mouse Exon arrays, analyzed at the gene level.

2012-05-31 | E-GEOD-30411 | biostudies-arrayexpress

Integrated omic analysis reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock

Project description:Circadian rhythmicity in renal function suggests a requirement for circadian adaptations in renal metabolism. We studied circadian changes in renal metabolic pathways using integrated transcriptomic, proteomic and metabolomic analysis performed on control mice and mice deficient in the circadian clock gene Bmal1 in the renal tubule (cKOt mice). Proteins were extracted from whole kidneys of 60 mice. Of these, 30 were conditional knockouts of Arntl (Bmal1) and 30 were of control genotype. They were housed under 12-hours light/12-hours dark cycles and were sacrificed at six different time points: zeitgeber time ZT 0, ZT 4, ZT 8, ZT 12, ZT 16, ZT 20 ( ZT 0 being the time of light on and ZT 12 the time of light off). Five replicates per genotype and time point were analysed.

2023-03-15 | PXD036803 | Pride

Effect of APAP-induced acute liver injury on WT and Nrf2KO zebrafish liver gene expression following 12 and 24 hours [RNA-Seq]

Project description:To investigate the transcriptional changes following acute liver injury, we exposed WT and Nrf2KO zebrafish larvae to APAP for 12 and 24 hours. We then dissected out zebrafish larval livers and pooled 20 livers per sample for RNA-seq.

2024-01-13 | GSE230829 | GEO

Liver Clock Rescue

Project description:Circadian clocks drive 24-h rhythms of physiology and behavior. The circadian clock of hepatocytes has been shown to regulate glucose metabolism, and we were interested if rescuing liver clock function can reverse metabolic impairments in hyperphagic/obese Clock-D19 mutant mice. We compared transcripomte regulation in livers (at Zeitgeber time ZT10) of wild-type (C57BL/6J) and Clock-D19 mice and Clock-D19 mice with genetic rescue of liver clock function using hydrodynamic tail vein injection of a WT-CLOCK expression plasmid

2017-03-31 | GSE94838 | GEO

Circadian Clock Properties of T2D Patients

Project description:The circadian system plays an essential role in regulating timing of body metabolism in humans. Indeed, circadian misalignments are strongly associated with high rates of metabolic disorders. Molecular makeup of the circadian oscillator can be deciphered in cells cultured in vitro, and these cellular rhythms are highly informative of the physiological circadian rhythm in vivo. We aimed at assessing molecular clock properties in dermal fibroblasts established from the skin biopsies of seventeen Type 2 diabetic obese and non-obese patients and eleven healthy controls. Following in vitro synchronization, primary fibroblast cultures were subjected to continuous assessment of circadian bioluminescence profiles based on lentiviral luciferase reporters. We observed a strong inverse correlation between HbA1c values and circadian period length within cells from the Type 2 diabetic group. RNA sequencing analysis conducted in this group samples revealed that ICAM1 encoding for the endothelial adhesion protein was differentially expressed between Type 2 diabetic compensated and non-compensated fibroblasts, and correlated with the period length. Furthermore, ICAM1 expression is driven by rhythmic CLOCK binding. We provide for the first time a potential molecular link between severity of Type 2 diabetes and circadian clock machinery, which paves a way for further mechanistic understanding of circadian oscillator changes upon Type 2 diabetes in humans.

| EGAS00001003622 | EGA

Clock rescue in the brain restores 12- and 24- hour rhythms in the liver

2012-06-01 | GSE30411 | GEO

Interactome of the circadian clock protein PERIOD2 in human U2OS osteosarcoma cells after the resetting of the circadian clock

Project description:Circadian rhythms are a series of endogenous autonomous 24-hour oscillations generated by the circadian clock. At the molecular level, the circadian clock is generated by a transcription-translation feedback loop, where BMAL1 and CLOCK transcription factors of the positive arm activate the expression of CRYPTOCHROME and PERIOD (PER) genes of the negative arm as well as the circadian clock-regulated genes. In this project, we aimed at finding the interactome of PER2 protein in human U2OS osteosarcoma cell line using proximity-dependent biotin identification (BioID) technique. U2OS clones overexpressing PER2-BioID2 or BioID2 were treated with dexamethasone in order to reset the circadian rhythm, and cells were then incubated in biotin-containing media for 12 hours to label the proteins in close proximity of PER2-BioID2. Samples were collected after 36 and 48 hours of the resetting to identify the labeled proteins by mass spectrometry. In addition to known interactors such as CRY1 and CRY2, many novel interactors were identified. In summary, we obtained a network of PER2 interactome and confirmed some of the novel interactions using classical the co-immunoprecipitation method.

2022-04-22 | PXD025179 | Pride

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