Project description:Microarray methylation (Infinium®HumanMethylation 450 BeadChip from Illumina) was performed on 11 normal and 9 chronic periodontitis (CP) patients Bisulphite converted DNA from the 20 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Project description:Microarray methylation (Infinium¨HumanMethylation 450 BeadChip from Illumina) was performed on 12 normal and 10 chronic periodontitis (CP) patients Bisulphite converted DNA from the 22 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Project description:Microarray methylation (Infinium® HumanMethylation450 BeadChip from Illumina) was performed on gingival tissue samples from 11 periodontitis cases and 12 age-matched healthy individuals. Bisulphite converted DNA from the 23 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Project description:To identify genes hypermethylated and transcriptionally downregulated, we have employed the Illumina Infinium HumanMethylation450 BeadChip and Agilent SurePrint G3 Human Gene Expression 8x60K. And we validated selected genes in cases and controls. eventually we estalished CIMP of MDS. Bisulphite converted DNA from the 4 patients and 4 controls were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Project description:Approximately 4 μg of DNA was isolated from blood of each of 16 subjects using the Qiagen DNEasy Blood and Tissue Kit. Of the 16 samples, 8 were from group 1 (CESD-H/TST-H; 5 female, 3 male) and 8 were from group 2 (CESD-H/TST-L; 5 female, 3 male). All DNA samples were confirmed to be of high purity (A260/280: 1.7-2.0). Pooled samples were prepared for each group by combining approximately 75 ng of DNA from each of the eight subjects. These two samples were submitted to the Yale Genomics Core for epigenome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip, which measures the level of methylation β (a value ranging from 0 to 1, where 0 represents a completely unmethylated site and 1 a completely methylated site) at each of the 485,577 CpG sites on the array. Illumina’s GenomeStudio software was used to calculate the degree of differential methylation by group for each CpG site on the array, and FDR-adjusted p-values (Q-values) were calculated for each site in order to adjust for multiple comparisons. CESD=depression score; TST=sleep score Blood-derived genomic DNA was isolated from 16 subjects; 8 each with high and low total sleep scores, respectively. DNA was pooled by group and genome-wide methylation profiling was performed.
Project description:Both genetic and epigenetic aberrations are linked by intricate crosstalk, and can either individually or in synergy lead to the development of cancer. Accumulating evidence suggests that epigenetic changes such as alterations in DNA methylation play a crucial role in ESCC. We performed a Illumina Infinium HumanMethylation450 BeadChip to examine the global methylation signature of esophageal squamous cell carcinoma of Chinese patients. DNA methylation profiles of esophageal squamous cell carcinoma (4 samples), paired adjacent normal surrounding tissues (4 samples) and normal esophagus mucosa from healthy individuals (4 samples) were generated using Infinium methylation 450K BeadChips from Illumina (Illumina, San Diego, USA).
Project description:To address the global impact of PARP-1 on DNA methylation, we treated cells with PJ34 (PARylation inhibitor) and isolated genomic DNA from vehicle and PJ34 treated cells. This DNA was bisulfite treated and hybridized to the Illumina infinium Methylation 450 Beadchip. We next used these RNA-seq data sets (control, PARP-1 KD and PARylation inhibited) to assess whether PARP plays a role in DNA methylation by assessing differential methylation patterns. PARP1 mediates methylation patterns. DNA from vehicle and PJ34 (PARylation inhibited) cells. 750ng of geneomic DNA was bisulfite converted and used for the Illumia infinium HD methylation assay.
Project description:We applied Illumina Human Methylation450K array to perform a genomic-scale single-site resolution DNA methylation analysis in neuronal and nonneuronal (primarily glial) nuclei separated from the orbitofrontal cortex of postmortem human brain. The findings were validated using enhanced reduced representation bisulfite sequencing. We identified thousands of sites differentially methylated (DM) between neuronal and nonneuronal cells. The DM sites were depleted within CpG island–containing promoters but enriched in predicted enhancers. Classification of the DM sites into those undermethylated in neurons (neuronal type) and those undermethylated in nonneuronal cells (glial type), combined with findings of others that methylation within control elements typically negatively correlates with gene expression, yielded large sets of predicted neuron-specific and non– neuron-specific genes. These sets of predicted genes were in excellent agreement with the available direct measurements of gene expression in human and mouse. We also found a distinct set of DNA methylation patterns that were unique for neuronal cells. In particular, neuronal-type differential methylation was overrepresented in CpG island shores, enriched within gene bodies but not in intergenic regions, and preferentially harbored binding motifs for a distinct set of transcription factors, including neuron-specific activity-dependent factors. Finally, non-CpG methylation was substantially more prevalent in neurons than in nonneuronal cells. Genomic DNA was isolated from FACS-sorted human brain neuronal and nonneuronal nuclei. DNA was bisulfite converted and hybridised to the Illumina Infinium 450K Human Methylation Beadchip array. Six subjects in two technical replicate expriments were analyzed.
Project description:Monocytes and granulocytes were isolated from blood of TB patients and household contacts. DNA was isolated and methylation profile was measured using Illumina HumanMethylation450. House-hold contacts were matched to TB patients by gender and age. From each subject, two profiles (monocytes and granulocytes) were collected.