Project description:A core task to understand the consequences of non-coding single nucleotide polymorphisms (SNP) is to identify their genotype specific binding of transcription factor (TF). Here, we generate a large-scale TF-SNP interaction map for a selection of 116 colorectal cancer (CRC) risk loci and validated TF binding to 10 putatively functional SNPs. Our data further revealed TF binding complexity adjacent to the 116 risk loci, adding an additional layer of understanding to regulatory networks associated with CRC relevant loci.
Project description:Separate transcription profiling of oocytes and granulosa cells for each follicle stage: primordial (PD), primary (PM), secondary (SC) follicles and the small antral stage (SA) obtained by Laser Capture Microdissection (LCM) and RNAseq. The purpose of this study was to describe global gene expression during early ovarian folliculogenesis for each follicular compartment, to identify differential and specific gene expression between the 2 follicular compartments and during follicular development, to investigate specific function and pathways and to explore bi-directional communication between oocytes and GC.
Project description:We correlated comprehensive T cell phenotyping data from peripheral blood to the corresponding genotype of different disease-associated and T cell related SNPs. This revealed significantly increased frequencies of naive CD4+ T cells (CD4+ TN) and T helper 17 (TH17) cells in carriers of intergenic SNP rs56258221 (BACH2/MIR4464) as compared to non-carriers. Functional experiments identified CD4+ TN from SNP-carriers to rather polarize towards pro-inflammatory subsets than into regulatory T cells (TREG). *** Due to data privacy concerns fastq files have not been uploaded ***
Project description:Obesity is a metabolic disease caused by environmental, genetic, and epigenetic factors. However, the epigenetic mechanisms of obesity are incompletely understood. The aim of our study was to identify skeletal muscle DNA methylation patterns in obesity. Muscle biopsies were obtained basally from lean (n=11) and obese (n=9) participants in combination with euglycemic hyperinsulinemic clamps to assess insulin sensitivity. We performed reduced representation bisulfite sequencing next generation methylation analysis on DNA isolated from vastus lateralis muscle biopsies.
Project description:Investigation of actin N-terminal acetylation status in zebrafish with knockout alleles for Naa80, the actin N-terminal acetyltransferase.
Project description:Affymetrix 6.0 SNP data for genome-wide linkage scans of a consanguineous Kuwaiti family with a combined immunodeficiency Peripheral blood or saliva were used for patients who had no history of hematopoietic stem cell transplant (HSCT). Fibroblasts cell lines were used as a source of DNA for individuals who received HSCT. Genomic DNA from 32 subjects (5 affected and 27 unaffected) from Family A was genotyped at 909,622 single nucleotide polymorphisms (SNPs) on the Genome-Wide Human SNP 6.0 Array (Affymetrix).