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: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: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 Human Airway Smooth muscle cells from subjects with and without asthma-effects of mimicking viral challenge
Project description:Human intelligence demonstrates one of the highest heritabilities among human quantitative traits. Phenotypically discordant monozygotic twins provide a way to identify loci responsible for normal-range intelligence. We conducted array-based genome-wide gene expression analysis aiming to identify genes displaying significant difference among monozygotic twin pairs manifesting between-co-twins IQ differences. Total RNA was isolated from B-lymphoblastoid cell lines and applied to Affymetirx arrays after reverse transcription. 17 twin pairs (34 subjects) were recruited in this study.
Project description:Probes with runs of four or more guanines (G-stacks) in their sequences can exhibit a level of hybridization that is unrelated to the expression levels of the mRNA that they are intended to measure. This is most likely caused by the formation of G-quadruplexes, where inter-probe guanines form Hoogsteen hydrogen bonds, which probes with G-stacks are capable of forming. We demonstrate that for a specific microarray data set using the Human HG_U133A Affymetrix GeneChip and RMA normalization there is significant bias in the expression levels, the fold change and the correlations between expression levels. These effects grow more pronounced as the number of G-stack probes in a probe set increases. Approximately 14% of the probe sets are directly affected. The analysis was repeated for a number of other normalization pipelines and two, FARMS and PLIER, minimized the bias to some extent. We estimate that ∼15% of the data sets deposited in the GEO database are susceptible to the effect. The inclusion of G-stack probes in the affected data sets can bias key parameters used in the selection and clustering of genes. The elimination of these probes from any analysis in such affected data sets outweighs the increase of noise in the signal.
Project description:Expression .CEL files from Affymetrix HG-U133A 2.0 arrays using DNA from 14 human cell lines derived from metastasized melanoma Study of global gene expression differences in malignant melanoma cell lines with or without specific abberations in BRAF NRAS or CDKN2A. UKRV-Mel-16a was wrongly described as Ma-Mel-16a in Blöthner et al. 2005