Project description:In order to examine the impact our probe filtering efforts might have on the analysis of real-world primary data, we analyzed clinical prostate cancer specimens. This included profiling of four prostate tumour tissue samples and four benign prostate tissues using the Illumina Infinium Human Methylation450 (HM450K bead array) BeadChip. These samples were used to explore the effects on analysis with and without a probe filtering.
Project description:In order to examine the impact our probe filtering efforts might have on the analysis of real-world primary data, we analyzed clinical prostate cancer specimens. This included profiling of four prostate tumour tissue samples and four benign prostate tissues using the Illumina Infinium Human Methylation450 (HM450K bead array) BeadChip. These samples were used to explore the effects on analysis with and without a probe filtering. Four tumour samples containing Gleason 6 cancer and four benign samples from other prostate glands containing Gleason 6 cancer were selected for study. Tissue samples were cryosectioned for histopathological assessment. Genomic DNA was extracted from the homogenized samples using the Allprep Micro Kit (Qiagen, CA, USA) following manufacturer’s instructions and bisulfite converted using the Zymo EZ DNA Methylation kit (Zymo Research Corporation, CA, USA). The resulting libraries were hybridized onto the Illumina HumanMethylation450 (HM450K bead array) BeadChip. Raw intensity data was generated using an iScan microarray reader (Illumina).
Project description:Genome wide DNA methylation profiling of HSTL in comparison to benign T-cell subsets. The Illumina Infinium 450k Human DNA methylation Beadchip was used.
Project description:Genome wide DNA methylation profiling of malignant, atypical and benign meningiomas samples. The Illumina infinium HumanMethylation450 beadchip kit was used, which assayed 450,000 potential methylation sites. Bisulphite converted DNA from the 23 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip.
Project description:Examination of DNA methylome patterns for potential subtypes in a larger cohort of ME/CFS samples using the Illumina Infinium HumanMethylation450 Beadchip Array Bisulfite-converted DNA from 25 samples were hybridised onto the Illumina Infinium HumanMethylation450 Beadchip Array
Project description:Genome wide DNA methylation profiling of Stage I Lung Adenocarcinoma and non-tumor adjacent tissues. The Illumina Infinium 27k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included tumor and adjacent non-tumor tissues excised from a cohort of 35 patients with Stage I Lung Adenocarcinoma. Candidate prognostic biomarkers were validated by pyrosequencing in independent cohorts. Total genomic DNA was bisulfite converted and hybridized to Infinium Human Methylation27Beadchips. Fluorescent signals were collated via Bead Studio software and converted into β-values. Illumina Bead Studio software output data were normalized using SSN (simple scaling normalization), to correct for dye bias and transformed into M-values (M = log2 intensity of methylated probe/ intensity of unmethylated probe), using the R package lumi.
Project description:Genome wide DNA methylation profiling of normal and tumoral urological tissues (Prostate, Kidney and Bladder). The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs in urological fresh frozzen tissue samples. Samples included morphologically normal samples of each tissue and tumor samples. Kidney: 6 normal and 17 tumor samples; Bladder: 5 normal and 25 tumor samples; Prostate: 5 Normal and 25 tumor samples.
Project description:Genome wide DNA methylation profiling of malignant, atypical and benign meningiomas samples. The Illumina infinium HumanMethylation450 beadchip kit was used, which assayed 450,000 potential methylation sites.
Project description:To investigate the anti-tumor function of compound H93 in the development of prostate cancer, we treated DU145 cell lines with H93, SAHA or DMSO. We then performed genome wide DNA methylation profiling analysis of cells after treatment. The Illumina Infinium MethylationEPIC BeadChip (850K BeadChip) was used to obtain DNA methylation profiles across approximately 850,000 CpGs.
Project description:Genome-wide DNA-methylation profiles of human lung cancer cell lines and normal lung cells were generated by Infinium bead chip technology DNA methylation patterns of over 480,000 CpG sites were analyzed in normal human bronchial epithelial cells (NHBEC) and three non small cell lung cancer cell lines (NSCLC: A427, A549 and H322) using bisulfite-based Illumina 450K BeadChip arrays
