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Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs

ABSTRACT: Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs

PROVIDER: PRJNA917779 | ENA |

REPOSITORIES: ENA

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Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs

Project description:Here we present clear patterns of age-associated changes in DNA methylation in the aquatic vertebrate species Xenopus tropicalis. We selected approximately 3500 sites highly correlated with age from WGBS data from 9 frogs of 3 different age groups (young, approx. 1 year old; mature, approx. 5 years old; old, approx. 9 years old - GSE221656) and designed probes for the development of cost effective targeted bisulfite sequencing (TBSeq) assay. Here, we present the TBSeq assay in sixteen different frogs as a pilot experiment to validate our previous findings.

2023-04-28 | GSE222107 | GEO

Age-associated DNA methylation changes in Xenopus frogs, and Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs

Project description:Age-associated DNA methylation changes in Xenopus frogs, and Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs

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Age-associated DNA methylation changes in Xenopus frogs

Project description:Here we present clear patterns of age-associated changes in DNA methylation in the aquatic vetebrate species Xenopus tropicalis. We generated nine whole-genome bisulfite sequencing (WGBS) datasets from three distinct age groups (young, approx. 1 year old; mature, approx. 5 years old; old, approx. 9 years old) to characterize the gene- and chromosome-scale changes.

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Xenopus frogs

Project description:Xenopus borealis, Xenopus laevis Raw sequence reads

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Tissue gene expression of Xenopus laevis J strain [tissue]

Project description:Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. This work is funded by Agency Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT; "Genome Science" Grant ID 221S0002). Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors)

2016-10-24 | E-GEOD-73419 | biostudies-arrayexpress

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Project description:Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

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2011-10-10 | E-GEOD-28510 | biostudies-arrayexpress

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