Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mus musculus

ABSTRACT: Comprehensive identification of the binding sites of CLOCK in the mouse liver using ChIP-Seq

PROVIDER: PRJDB2806 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR013052.fastq.gz	Fastqsanger.gz
	DRR013053.fastq.gz	Fastqsanger.gz
	DRR013054.fastq.gz	Fastqsanger.gz
	DRR013055.fastq.gz	Fastqsanger.gz
	DRR013056.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

Mus musculus strain:C57BL/6J

Project description:Comprehensive identification of the binding sites of DBP/E4BP4 in the mouse liver using ChIP-Seq

| PRJDB7796 | ENA

Mus musculus

Project description:Identification of Cux2 binding sites in female and male mouse liver

| PRJNA151645 | ENA

Mus musculus

Project description:Identification of Hnf6 binding sites in male and female mouse liver

| PRJNA257278 | ENA

Mus musculus

Project description:Comprehensive identification of circadian genes in the mouse liver using RNA-Seq

| PRJDB2805 | ENA

Supplement data of project: A proteomics landscape of circadian clock in mouse liver

Project description:As a circadian organ, liver executes diverse functions in different phase of the circadian clock. This process is believed to be driven by a transcription program. Here, we present a TF DNA-binding activity centered multi-dimensional proteomics landscape, including DNA-binding activity of TFs, the phosphorylation pattern, ubiquitylation pattern, the nuclear sub-proteome, the whole proteome as well as the transcriptome, to portrait the hierarchical circadian clock network of mouse liver. The TF DNA-binding activity indicates diurnal oscillation in four major pathways, immune response, glucose metabolism, fatty acid metabolism, and the cell cycle. We also isolated the mouse liver Kupffer cells and measured their proteomes in the circadian clock to reveal cell type resolved circadian clock. These are the most comprehensive datasets for circadian clock in the mouse liver and provided the richest data resource for the understanding of mouse liver physiology around the circadian clock.

2018-06-25 | PXD008862 |

A proteomics landscape of circadian clock in mouse liver

2018-06-25 | PXD008771 |

Chromatin immunoprecipitation of human cell line HEPG2 to identify liver specific transcription factor binding sites

Project description:Identification of liver transcription factors binding sites by ChIP-chip using HepG2 cells. Inference of binding sites at base pair resolution was achieved by using bioinformatic tools on the generated data sets.

2005-10-01 | E-MEXP-452 | biostudies-arrayexpress

Genome-Wide And Phase-Specific DNA-Binding Rhythms Of BMAL1 Control Circadian Output Functions In Mouse Liver

Project description:Using chromatin immuno-precipitation (ChIP) combined with deep sequencing (ChIP-seq) we obtained a time resolved and genome-wide map of BMAL1 binding in mouse liver, which allowed to identify over two thousand binding sites with peak binding narrowly centered around Zeitgeber time (ZT) 6. Annotation of BMAL1 targets confirms carbohydrate and lipid metabolism as the major output of the circadian clock in mouse liver. Moreover, transcription regulators are largely overrepresented, several of which also exhibit circadian activity. Genes of the core circadian oscillator stand out as strongly bound, often at promoter and distal sites. Genomic sequence analysis of the sites identified E- boxes and tandem E1-E2 consensus elements. Electromobility shift assays (EMSA) showed that E1-E2 sites are bound by a dimer of BMAL1/CLOCK heterodimers with a spacing-dependent cooperative interaction that was further validated in transactivation assays. BMAL1 target genes showed cyclic mRNA expression profiles with a phase distribution centered at ZT10. Importantly, sites with E1-E2 elements showed tighter phases both in binding and mRNA accumulation. Finally, comparing the temporal accumulation of precursor mRNA and mature mRNA helped distinguish direct BMAL1 targets from targets with more complex regulation, and showed how transcriptional and post-transcriptional regulation contribute differentially to circadian expression phase. Together, our analysis of a dynamic protein-DNA interactome uncovered how genes of the core circadian oscillator are wired together and drive phase-specific circadian output programs in a complex tissue. ChIP-Seq of BMAL1 in mouse liver during one circadian cycle at 4 hour time resolution presented in this Series (GSE26602). mRNA profiling data used in this study are already published (Kornmann et al, PLoS Biol 2007) and have been deposited on ArrayExpress repository (accession number: E-MEXP-842).

2011-02-23 | E-GEOD-26602 | biostudies-arrayexpress

Mus musculus

Project description:Comprehensive identification of rhythmically expressed miRNAs in the mouse liver using small RNA-Seq

| PRJDB2807 | ENA

Mus musculus

Project description:Identification of PTBPs RNA binding sites in mouse brain

| PRJNA336372 | ENA