Project description:DNA methylation profiling of IAS subjects Lymphoblasts RNA isolated from Iowa Adoption Study participants to compare the relationship between DNA methylation and gene expression on a genome-wide scale
Project description:Transcriptional profiling of IAS subjects Lymphoblasts RNA isolated from Iowa Adoption Study participants to compare the relationship between DNA methylation and gene expression on a genome-wide scale
Project description:Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions, demonstrating that methylation of transposable elements is temperature sensitive and associated with genetic polymorphism in both cis and trans, whereas gene body methylation is highly correlated with climate of origin and associated with genetic polymorphism in trans that shows evidence of local adaptation. While genome-wide surveys of naturally occurring DNA methylation have been published previously, the degree of genetic control revealed here is unprecedented. Furthermore, the observation that DNA methylation is associated with climate, and is apparently adaptively important, is completely novel. Bisulfite sequencing of 152 Swedish Arabidobsis accessions grown at 10 C and 121 grown at 16 C
Project description:DNA methylation profiling of IAS subjects Lymphoblasts RNA isolated from Iowa Adoption Study participants to compare the relationship between DNA methylation and gene expression on a genome-wide scale
Project description:Lung cancer is a highly heterogeneous disease in terms of both underlying genetic lesions and response to therapeutic treatments. We performed deep whole genome sequencing and transcriptome sequencing on 19 lung cancer cell lines and 3 lung tumor/normal pairs (provisional dbGaP accession number; phs000299.v2.p1). Overall, our data show that cell line models exhibit similar mutation spectra to human tumor samples. Taken together, these data present a comprehensive genomic landscape of a large number of lung cancer samples and further demonstrate that cancer specific alternative splicing is a widespread phenomenon that has potential utility as therapeutic biomarkers. Nineteen non-small cell lung cancer cell lines were assayed for genotype, copy number and LOH using Illumina Omni2.5-4 arrays, GenomeStudio V2011.1, and a modified version of the PICNIC (PMID 19837654) algorithm.
Project description:To identify genes activated under CoCl2 treatment of a cancer cell line in an Sp1 dependent manner, we performed cDNA microarray analysis with an ovarian cancer cell line, in which Sp1 is silenced via RNA interference. Cells were transfected with scramble or Sp1 siRNA and cultured for 40 h. Cells were further cultured for 4 h under 0.5 mM CoCl2 exposure. Total RNA was isolated for cDNA microarray analysis.
Project description:Genome wide DNA methylation profiling of epidermal and dermal samples obtained from sun-exposed and sun-protected body sites from younger (<35 years old) and older (>60 years old) individuals. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in dermal and epidermal samples. Samples included 10 younger sun protected dermal samples, 10 younger sun exposed dermal samples, 10 older sun protected dermal samples, 10 older sun exposed dermal samples, 9 younger sun protected epidermal samples, 9 younger sun exposed epidermal samples, 10 older sun protected epidermal sample, 10 older sun exposed epidermal samples. Bisulphite converted DNA from the 78 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.
Project description:Map the location of the dityrosine bond in the purified crosslinked sample(DT-preF) by LC-ESI-MS/MS.The uncrosslinked protein (preFC) was used for comparison.
Project description:Investigation of whole genome gene expression level changes in a Clostridium difficile fur (ferric uptake regulator) mutant, compared to the wild type strain 630 erm. The fur mutant analyzed in this study is further described in Ho and Ellermeier (2015) J. Bacteriology A microarray study using total RNA recovered from three separate wild type cultures of Clostridium difficile 630 erm strain and three separate cultures of a fur mutant strain (ltrA::ermR) were grown in Tryptone-Yeast Extract medium containing 0.25 mM ferric chloride . Each chip measures the expression level of 3,786 of the 3,787 open reading frames of the C. difficile 630 genome with 18 probes (60 oligomers each) for each gene.