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Genome-scale methylation changes induced by photoperiods in Nasonia vitripennis

ABSTRACT: Seasonal photoperiodic changes have strong impact on development in Nasonia vitripennis. Here, Using high-throughput Reduced Representation Bisulfite Sequencing (RRBS) and single-molecule-based sequencing, we generated DNA methylation maps of female wasps maintained in long vs short day. We have identified differential methylated loci that encode the photoperiodic change. analysis of DNA methylation in female wasps maintained in long vs short day, using RRBS followed by Illumina sequencing

ORGANISM(S): Nasonia vitripennis

SUBMITTER: Eran Tauber

PROVIDER: E-GEOD-44869 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-scale methylation changes induced by photoperiods in Nasonia vitripennis

Project description:Seasonal photoperiodic changes have strong impact on development in Nasonia vitripennis. Here, Using high-throughput Reduced Representation Bisulfite Sequencing (RRBS) and single-molecule-based sequencing, we generated DNA methylation maps of female wasps maintained in long vs short day. We have identified differential methylated loci that encode the photoperiodic change.

2014-09-01 | GSE44869 | GEO

DNA methylation analysis by RRBS in germ cells of mice exposed to Vinclozolin

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2015-06-22 | E-GEOD-65784 | biostudies-arrayexpress

Tet and TDG Mediate DNA Demethylation Essential for MET in Somatic Cell Reprogramming

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2014-02-19 | E-GEOD-52741 | biostudies-arrayexpress

Genome-scale DNA methylation maps of mouse chromaffin cells with or without Sdhb knock-out.

Project description:We report the analysis of DNA methylation in mouse chromaffin cell lines using reduced representation bisulfite sequencing (RRBS). We compared DNA methylation profiles of cell lines with or without a knock-out of Sdhb gene, showing that Sdhb disruption results in a hypermethylator phenotype. Reduced representation bisulfite sequencing of 4 mouse chromaffin cell samples (2 Sdhb wild-type and 2 Sdhb knock-out).

2013-05-06 | E-GEOD-44350 | biostudies-arrayexpress

Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Embryonic Stem Cells (RRBS)

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2016-08-02 | E-GEOD-84103 | biostudies-arrayexpress

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Project description:We quantified the targets and kinetics of DNA methylation acquisition in mouse embryos, and determined the contribution of the de novo methyltransferases DNMT3A and DNMT3B to this process. We provide single-base maps of cytosine methylation by RRBS from the blastocysts to post-implantation stages and in embryos lacking DNMT3A or DNMT3B activity, and performed RNA-Seq in embryos lacking DNMT3B activity. We sequenced RRBS libraries prepared from genomic DNA isolated from embryos at consecutive stages of development between E3.5 and E11.5,and adult differentiated cells (sperm, liver). We performed RRBS on blastocysts at E3.5/E4.5, dissected epiblasts at E5.5/E6.5/E7/5, whole embryos at E8.5/E10.5 and limbs at E11.5. RRBS experiments in Dnmt3a-/- and Dnmt3b-/- embryos were performed in biological duplicates on individual embryos. We sequenced RNA-Seq libraries prepared from total RNAs of three WT and Dnmt3b-/- littermate embryos collected at E8.5.

2014-11-14 | E-GEOD-60334 | biostudies-arrayexpress

DNA methylation profiling to investigate how Tet1 controls maintenance DNA methylation via the regulation of Dppa3 in ESCs

Project description:DNA methylation profiling using RRBS in wild type and Dppa3 knockout ESCs.

2020-09-30 | E-MTAB-6800 | biostudies-arrayexpress

Methylation disorder in CLL

Project description:We performed RRBS and WGBS on primary human chronic lymphocytic leukemia and normal healthy donor B cell samples Due to patient privacy concerns, the raw data is being made available via controlled access in dbGaP (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000435.v1.p1). cross-sectional/longitudinal

2015-01-01 | E-GEOD-58889 | biostudies-arrayexpress

FBXL10 and the Protection of Polycomb-bound Genes from Hypermethylation (RRBS)

Project description:Nearly all CpG-dense promoters are occupied by the multi-domain chromosomal protein FBXL10. We show here that complete inactivation of the Fbxl10 gene leads to dense de novo methylation only of the promoters that are co-occupied by both FBXL10 and by Polycomb Repressive Complexes; this results in pervasive defects in embryonic development and death of homozygous Fbxl10 mutant embryos at midgestation. Deletion of key components of Polycomb Repressive Complexes 1 and 2 did not lead to ectopic de novo methylation. These results indicate that FBXL10 defends Polycomb-occupied promoters against ectopic de novo methylation. FBXL10 is the first reported factor whose loss leads to a gain in genomic DNA methylation. DNA methylation analysis using RRBS and expression analysis using RNA-seq was performed on WT and Fbxl10T/T ES cells.

2015-04-06 | E-GEOD-65580 | biostudies-arrayexpress

DNA methylation changes induced by overexpression of IDH1mut or treatment with 2HG in the sorted mouse bone marrow cells

Project description:Mutations in the enzymes IDH1 and IDH2 have been identified in a wide variety of tumors like glioma, chondrosarcoma, thyroid cancer, lymphoma, melanoma, and in acute myeloid leukemia. Mutated IDH1/2 produces the metabolite 2-hydroxyglutarate (2HG), which interferes with epigenetic regulation of gene expression, and thus may promote tumorigenesis. HoxA9 immortalised bone marrow cells from C57BJ/6 mice were tranduced with either empty vector or pSF91-IDH1wt-IRES-EGFP, or pSF91-IDH1mut-IRES-GFP and transplanted in irradiated recipient mice. Alternatively, HoxA9 immortalised cells transduced with empty vector transplanted mice were treated with R-2HG at dose of 1mg/day for four weeks. Four weeks after transplantation/treatment GFP+ cells were sorted from mouse bone marrow, from which total DNA was extracted and subjected to Reduced Representation Bisulfite Sequencing (RRBS) to determine the genome-wide methylation signature.

2016-06-01 | E-GEOD-77828 | biostudies-arrayexpress

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