Gene expression during mouse OS25 ES cell differentiation. Mus musculus

Position within chromosome territories, and localisation at transcription factories, are two facets of nuclear organisation that have been associated with active gene expression. However, there is still debate about whether this organisation is a cause or consequence of transcription. We induced looping out from chromosome territories (CTs), by the activation of Hox loci during differentiation, to investigate consequences on neighbouring loci. This microarray study aims at analyzing the expression of genes close to Hoxb and Hoxd clusters in parallel with their nuclear position. Overall design: OS25 mouse ES cells were differentiated using retinoic acid in two independent experiments, and control undifferentiated cells were also cultured. For each experiment, labelled cDNAs were prepared from undifferentiated and differentiated cells and hybridized together on VUMC MACF Mouse 38K oligo v64 microarrays. Labelling dyes (Cy3 / Cy5) were swapped for cDNAs from the second differentiation experiment.