Xenopus tropicalis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA121789 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Background: Chromatin immunoprecipitation combined with genome tile path microarrays or deep sequencing can be used to study genome-wide epigenetic profiles and the transcription factor binding repertoire. Although well studied in a variety of cell lines, these genome-wide profiles have so far been little explored in vertebrate embryos. Principal findings: Here we report on two genome tile path ChIP-chip designs for interrogating the Xenopus tropicalis genome. In particular, a whole-genome microarray design was used to identify active promoters by close proximity to histone H3 lysine 4 trimethylation. A second microarray design features these experimentally derived promoter regions in addition to currently annotated 5â ends of genes. Conclusions: A whole-genome and a dedicated promoter microarray design was developed which can be used to study epigenetic phenomena and transcription factor binding in developing Xenopus embryos. H3K4me3 and TBP ChIP-chip on Xenopus tropicalis tiling arrays
2010-05-17 | E-GEOD-19413 | biostudies-arrayexpress
Project description:Background: Chromatin immunoprecipitation combined with genome tile path microarrays or deep sequencing can be used to study genome-wide epigenetic profiles and the transcription factor binding repertoire. Although well studied in a variety of cell lines, these genome-wide profiles have so far been little explored in vertebrate embryos. Principal findings: Here we report on two genome tile path ChIP-chip designs for interrogating the Xenopus tropicalis genome. In particular, a whole-genome microarray design was used to identify active promoters by close proximity to histone H3 lysine 4 trimethylation. A second microarray design features these experimentally derived promoter regions in addition to currently annotated 5’ ends of genes. Conclusions: A whole-genome and a dedicated promoter microarray design was developed which can be used to study epigenetic phenomena and transcription factor binding in developing Xenopus embryos.
2009-12-17 | GSE19413 | GEO
Project description:Enhancer chromatin signatures predict Smad2/3 binding in Xenopus
| PRJNA242234 | ENA
Project description:DNA methylation clocks have been widely used for accurate age prediction, but most studies have been carried out on mammals. Here we present an epigenetic clock for the aquatic frog Xenopus tropicalis, a widely used model organism in developmental biology and genomics. To construct the clock, we collected DNA methylation data from 192 frogs using targeted bisulfite sequencing at genomic regions containing CpG sites previously shown to have age-associated methylation in Xenopus. We found highly positively and negatively age-correlated CpGs are enriched in heterochromatic regions marked with H4K20me3 and H3K9me3. Positively age-correlated CpGs are enriched in bivalent chromatin and gene bodies with H3K36me3, and tend to be proximal to lowly expressed genes. These epigenetic features of aging are similar to those found in mammals, suggesting evolutionary conservation of epigenetic aging mechanisms. Our clock enables future aging biology experiments that leverage the unique properties of amphibians.
2025-05-17 | GSE292839 | GEO
Project description:Comprehensive identification and characterization of the binding sites in the Xenopus tropicalis gastrula.
| PRJDB2633 | ENA
Project description:Comprehensive indentification and characterization of the binding sites in the Xenopus tropicalis gastrula.
| PRJDB1932 | ENA
Project description:Comprehensive identification and characterization of the binding sites in the Xenopus tropicalis gastrula.
| PRJDB1768 | ENA
Project description:Comprehensive identification and characterization of the binding sites in the Xenopus tropicalis gastrula.
| PRJDB2709 | ENA
Project description:Exploring Enhancers and Promoters in Xenopus tropicalis Osteoblasts through Chip-Seq analysis
| PRJNA1056467 | ENA
Project description:Comprehensive identification and characterization of the binding sites on TLE in the Xenopus tropicalis gastrula.
| PRJDB2671 | ENA