Ontology highlight
ABSTRACT:
PROVIDER: PRJNA578952 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To assess variation and inheritance of genome-wide patterns of DNA methylation simultaneously in humans, we applied reduced representation bisulfite sequencing (RRBS) to somatic DNA from six members of a three-generation family. Reduced representation bisulfite sequencing was applied to genomic DNA from leukocytes of 6 family members and two unrelated individuals.
2011-07-01 | E-GEOD-30253 | biostudies-arrayexpress
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
Project description:Cytosine base modifications 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) are present in mammalian DNA. Here, reduced bisulfite sequencing is developed for quantitatively sequencing 5fC at single-base resolution. This method is then applied with oxidative bisulfite sequencing to gain a map of 5mC, 5hmC and 5fC in mouse embryonic stem cells. 12 samples, reduced representation bisulphite treatment: 4 replicates each for bisulphite (BS), oxidative BS (oxBS) and reduced BS (redBS) for the detection of 5mC, 5hmC and 5fC. Mouse (strain B6C) embryonic stem cells.
2014-04-08 | E-GEOD-56572 | biostudies-arrayexpress
Project description:Here we used Illumina NGS for high-throughput profiling of the DNA methylome in two human colon cancer derived cell lines, two human normal bone marrow CD34+ controls and in five human Acutre Myeloid Leukeima patient samples. These data can be used to determine the CpG cytosine methylation pattern at base pair resolution in each sample and to determine differentially methylated cytosines and regions between samples Reduced Representation Bisulfite Sequencing (RRBS) and Extended Reduced Representation Bisulfite Sequencing (ERRBS) on genomic DNA. We used colon cancer cell lines (two) to establish reproducbility and range of assay sensitivity. We used Acute Myeloid Leukemia patient samples and CD34+ bone marrow cells as controls to determine the methylome pattern in the patient samples
2012-06-01 | E-GEOD-37454 | biostudies-arrayexpress
Project description:Reduced representation bisulfite sequencing (RRBS) of hematopoeitic stem/progenitor cells and mature B-cells from wild-type mice and mice transiently expressing Bcl6 under control of the Sca1 promoter. CBAxC57BL/6J mice were engineered to transiently express a Bcl6 cDNA in hematopoeitic stem/progenitor cells under control of the Sca1 promoter and then delete the transgene by cre-mediated recombination upon expression of Cd79a (Sca1-BCL6?). Hematopoeitic stem/progentior cells (HSPC, Sca1+Lin-) from the bone marrow and mature B-cells (B220+) from the peripheral blood were isolated from these mice and wild-type CBAxC57BL/6J mice by fluorescence activated cell sorting. Cells from 6-9 mice were pooled, for a total of 4 experimental conditions. DNA was extracted for each condition and analyzed by reduced representation bisulfite sequencing.
2014-03-28 | E-GEOD-56310 | biostudies-arrayexpress
Project description:Reduced Representation Bisulfite Sequencing in Smchd1MD43/MD43 and Smchd1+/+ neural stem cells.
2021-05-08 | GSE174079 | GEO
Project description:RRBS (Reduced Representation Bisulfite Sequencing) of HL60
| PRJNA154871 | 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 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