Project description:The purpose of this experiment is to characterize changes in the transcriptome and epigenome in diet-associated liver cancer. For that we used the DIAMOND mice as a model organism and performed RNA-seq and H3K27Ac and H3K27Me3 ChIP-seq in livers from control mice (fed with a regular diet) and livers and tumours from western diet fed mice.
Project description:The purpose of this experiment is to characterize changes in the transcriptome and epigenome in diet-associated liver cancer. For that we used the DIAMOND mice as a model organism and performed RNA-seq and H3K27Ac and H3K27Me3 ChIP-seq in livers from control mice (fed with a regular diet) and livers and tumours from western diet fed mice.
Project description:We analyzed the transcriptional effects of transgenic expression of our erythroid-specific codon-optimized GATA1 lentiviral vector in differentiating red blood cells of patients diagnosed with Diamond-Blackfan anemia.
Project description:Gene expression analysis from erythroid progenitors (CD34+/CD71(high)/CD45- mononuclear cells from the bone marrow) of patients with Diamond-Blackfan anemia (due to RPS19 mutations) and control individuals.
Project description:Epigenomic profiling by ChIP-seq is a prevailing methodology used to investigate chromatin-based regulation in biological systems, such as human disease, yet the lack of an empirical methodology to normalize amongst experiments has limited the usefulness of this technique. Here we describe a “spike-in” normalization method that allows the quantitative comparison of histone modification status across cell populations using defined quantities of a reference epigenome. We demonstrate the utility of this method in measuring epigenomic changes following chemical perturbations and show how control normalization of ChIP-seq experiments enables discovery of disease-relevant changes in histone modification occupancy. ChIP-Seq of histone modifications H3K79me2 and H3K4me3 in human samples treated with EPZ-5676 with/without reference epigenome spike-in.