Whole-genome DNA methylation maps for primate tissues
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ABSTRACT:
PROVIDER: PRJNA272127 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below.
2017-01-22 | GSE64830 | GEO
Project description:To examine the Boea hygrometrica genome methylation landscape and assess its functional significance during dehydration, we generated the first single-base resolution genome methylation maps for leaf tissues of hydrated, dehydrating to 70% RWC and dehydrating to 10% RWC (desiccating). The overall density of methyl-cytosine was not broadly altered by dehydration. There is, however, a small increase in intensity both for the whole genome and regionally during the first dehydration step (70% RWC) returning to near hydrated levels as leaves desiccate. We identified 5575 differentially methylated region-related genes during dehydration. The finding may provide an important clue for exploring molecular mechanisms and the regulation of desiccation tolerance at the whole-genome level.
2016-07-13 | GSE48904 | GEO
Project description:Comparison of DNA methylation in human tissues
| PRJNA171701 | ENA
Project description:The aim of this study was to characterize the genome-wide DNA methylation profiles of chimpanzee trabecular bone samples (n=4), identify how they relate to aspects of femur bone morphology, and assess how these epigenetic patterns relate to those in other primate taxa. The Illumina Infinium MethylationEPIC array was used to assess genome-wide methylation patterns.
2020-03-09 | GSE94677 | GEO
Project description:We report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput Reduced Representation Bisulfite Sequencing (RRBS) and single-molecule-based sequencing, we generated DNA methylation maps covering the vast majority of CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for murine embryonic stem (ES) cells, ES-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of ES-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumors. More generally, the results establish RRBS as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine. Keywords: High-throughput Reduced Representation Bisulfite Sequencing (RRBS), Illumina, cell type comparison Reduced representation bisulfite sequencing (MspI,~40-220bp size fraction) of 18 murine cell types. Raw sequence data files for this study are available for download from the SRA FTP site at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000179
2008-07-06 | E-GEOD-11034 | biostudies-arrayexpress
Project description:It has long been hypothesized that changes in gene regulation have played an important role in primate evolution. However, despite the wealth of comparative gene expression data, there are still only few studies that focus on the mechanisms underlying inter-primate differences in gene regulation. In particular, we know relatively little about the degree to which changes in epigenetic profiles might explain differences in gene expression levels between primates. To this end, we studied DNA methylation and gene expression levels in livers, hearts, and kidneys from multiple humans and chimpanzees. Genome wide DNA methylation profiling of heart, kidney, and liver samples from humans and chimpanzees. The Illumina Infinium 27K Human DNA Methylation BeadChip v1.2 was used to compare DNA methylation profiles across approximately 10,575 CpG sites in human and chimpanzee tissue samples. Samples included 6 human livers, 6 human kidneys, 6 human heart, 6 chimpanzee livers, 6 chimpanzee kidneys, and 6 chimpanzee hearts. Two techical replicates of bisulfite converted DNA from each of the 36 samples was hybridized to the Illumina HumanMethylation27 Beadchip. We limited our analysis to the 10,575 probes that were a perfect sequence match to both the human and chimpanzee genomes and which were associated with genes for which we had previously collected expression measurements across the three tissues.
2011-02-25 | E-GEOD-26033 | biostudies-arrayexpress
Project description:DNA methylation maps of mouse NSCs treated with naloxone
| PRJNA420451 | ENA
Project description:We report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput Reduced Representation Bisulfite Sequencing (RRBS) and single-molecule-based sequencing, we generated DNA methylation maps covering the vast majority of CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for murine embryonic stem (ES) cells, ES-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of ES-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumors. More generally, the results establish RRBS as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine. Keywords: High-throughput Reduced Representation Bisulfite Sequencing (RRBS), Illumina, cell type comparison
2008-07-06 | GSE11034 | GEO
Project description:Whole-genome DNA methylation maps for human and chimpanzee peripheral blood leukocytes (PBLs).
| PRJNA272130 | ENA
Project description:The aim of this study was to characterize the genome-wide DNA methylation profiles of nonhuman primate trabecular bone samples (n=58), identify how they relate to aspects of femur bone morphology, and assess how these epigenetic patterns vary between taxa. The Illumina Infinium MethylationEPIC array was used to assess genome-wide methylation patterns.
2020-03-15 | GSE103287 | GEO