Project description:Illumina bead array data from TCAM2/14411H/2102EP cell lines for mRNA expression. Lines are treated with either MMC or a combination of miR-100-5p and miR-125b-5p (combo), RNA extracted at day2. There are also some untreated controls at day 7.
Project description:Genome-wide DNA methylation profilinf from 67 non syndromic cleft lip and palate samples and controls using whole-blood DNA and Illumina Infinium Human Methylation 450K Bead array, in which over 485000 CpGs sites were analysed per sample
Project description:Human Tonsillar B cells were isolated and transfected with miR-29 mimic molecules or transfection controls. B cells were subsequently cultured in class switching media for 24 hours and subjected to transcriptome analysis using the Illumina HumanHT-12 v4 Expression BeadChip array platform. B cells derived from 3 donors are submitted.
Project description:Genome wide DNA methylation profiling of wild type and PPM1D mutant astrocytes and patient-derived DIPG cell lines. The Illumina Human EPIC Bead Array (850k) platform was used to obtain methylation beta values of over 850k CpG sites throughout the genome across a panel of DIPG cell lines.
Project description:This dataset contains 9 Illumina array spots representing 3 different treatment conditions of human mesenchymal cells. First two conditions in quadruplicate and third condition on single array. The data are intended to support blima package as testing data included in blimaTestingData package available at https://bitbucket.org/kulvait/blima page. The package was developed to make analysis of Illumina bead level data possible without summarizing them to the level of probes prior to differential expression testing.
Project description:Genome wide DNA methylation profiling of four control and cancer cell lines where apoptosis was induced using BH3 mimetics. The Illumina Human MethylationEPIC methylation profiling array was used to obtain DNA methylation profiles across approximately 850,000 CpGs. 8 samples were from treated cells harvested at two different time points representing early and late apoptotic stages, and 4 samples were controls combined from the two timepoints. 4 additional samples was left over DNA from the Nalm6 cell line ran on the array to fill up the bead chips. Data analysis will be presented in the manuscript "HPV-induced host epigenetic reprogramming is lost upon progression to high-grade cervical intraepithelial neoplasia" accepted for publication in the International Journal for Cancer.
Project description:TGFβ is one of most intensively studied regulators of extracellular matrix formation, and has been implicated in the development of pulmonary fibrosis in different models. However, little is know about the role of miRNAs in TGFβ mediated fibrogenic gene regulation. By using miRNA qRT-PCR array, we have identified miRNAs whose expression are regulated by TGFβ in IMR-90 cells. Among those down-regulated miRNAs are miR-29 family members. Knockdown miR-29 in IMR-90 cells results in up-regulation of a large number of extracellular matrix and fibrogenic genes including family members of collagen, laminin, integrin, ADAM and MMP, many of them are predicted or confirmed miR-29 targets. Hierarchichal clustering analysis of mRNA array data revealed that many extracellular matrix and fibrogenic genes up-regulated by TGFβ in IMR-90 cells, are also up-regulated in miR-29 KD cells. Moreover, the similar set of extracellular matrix and fibrogenic genes is also significantly up-regulated in bleomycin treated mouse lungs. Together, our data strongly suggest that downstream of the TGFβ, miR-29 is a master modulator of genes involved in extracellular matrix formation and might play a significant role in pulmonary fibrosis.
Project description:DNA methylation markers in thyroid tumor We used Illumina HumanMethylation EPIC bead array containing over the 850,000 CpG sites in 34 thyroid normal and tumor samples to identify thyroid subtype-specfic DNA methylation markers.
