Project description:Inhibitors of DNA methyl transferase (DNMT) might be useful for treating cardiac hypertrophy by preventing de novo methylation and reduced transcription of anti-hypertrophic genes. This approach had been tested, but without a detailed phenotypic and methylation analysis. Here, we subjected rats to pressure overload and treatment with the DNMT inhibitor N-phthalyl-L-tryptophan (RG108) and analysed DNA methylation by cardiomyocyte (CM)-specific reduced representation bisulphite sequencing (RRBS).
Project description:Loss of Tet1 expression causes global 5mC and 5hmC changes in stem and progenitor cells in mice and causes enhanced Pro-B cell self-renewal, increased DNA damage and B-lymphomageneis. In this study we performed reduced representative bisulfite sequencing (RRBS) of DNA from WT and Tet1 KO LSK cells. DNA methylation sequencing was performed and analyzed using an enhanced reduced representation (ERRBS) methodology as previously described. DNA was extracted from purified LSK cells of 6-month old WT and Tet1 KO mice, Bisulphite treatment was performed using the EZ DNA Methylation Kit (Zymo Research). Libraries were amplified according to illumina protocols and sequenced on an Illumina HiSeq2500 machine DNA methylation profiling of LSK cells in WT and Tet1 KO mice.
Project description:In this study, to obtain a clear picture of drought mechanism involved in two distinctive chickpea genotype, the aim was to identify the DNA methylation patterns which potentially regulate drought tolerance/sensitivity of these selected genotypes. The leaf tissues from the shoot apical meristem from drought sensitive and drought tolerant genotypes were used for RRBS (Reduced representation bisulphite sequencing) under drought stress. The sequencing data was analysed using Bismark and methylkit to recall the methylation levels in control and samples for both genotypes and identify differentially methylated regions.
Project description:Genome wide DNA methylation profiling of whole blood in schizophrenia patients and healthy subjects. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Raw data included 325 schizophrenia patients (2) and 394 controls (1) from Dutch descent. One sample was excluded since it was a bipolar patient, indicated by 3 in diseaseStatus column. The column used_in_analysis shows the samples that were used in our study. The excluded samples failed quality control. Normalized data are also included in the non_normalized.txt (i.e. AVG_Beta column). Bisulphite converted DNA from 720 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip [Publication: Horvath et al., Genome Biology, Special Edition]
Project description:Genome wide DNA methylation profiling of whole blood in schizophrenia patients and healthy subjects of different ages. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 62 schizophrenia patients and 33 healthy subjects from Dutch descent. Bisulphite converted DNA from the 96 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Publication: Steve Horvath, Yafeng Zhang, Peter Langfelder, René S. Kahn, Marco P.M. Boks, Kristel van Eijk, Leonard H. van den Berg, Roel A. Ophoff. Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biology. Special Edition. The raw data (non-normalized Unmethylated and Methylated signal intensities) are not available.
Project description:Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression
Project description:Bisulphite sequencing enables DNA methylation analysis of every cytosine residue. We have optimized conditions for combining chromatin immunoprecipation (ChIP) with high throughput bisulphite sequencing to study the relationship between histone modifications and DNA methylation.
