Global comparison of mouse ES cell lines derived from blastocysts and preblastocysts.. Mus musculus

Standard mouse ES cell derivation protocols use blastocysts at 3.5 dpc, but the efficiency of successful line derivation is low in commonly-used inbred strains, and much lower in other mouse strains. By using 2-cell zona pellucida-free embryos, culturing them on embryonic feeder cells, and passaging the outgrowths in several different media formulations, we have dramatically improved mouse ES cell line derivation efficiency. Mouse ES cell lines derived from blastocyst outgrowths using standard procedures were compared to preblastocyst (2-cell outgrowth)-derived lines, each derived in three different media formulations, using the genome-scale MEEBO gene expression oligo probe set. The overall goal of this microarray study is to determine the overall similarity between cell lines derived using the two methods, in terms of gene expression, as well as to identify important differences. Additionally, we hope to identify effects of the media formulation on gene expression in the cell lines. Overall design: Seven-condition experiment (two cell types, three derivation conditions, plus one control cell line). 2 biological replicates for each cell line, independently grown and harvested. One dye-swapped pair of arrays per replicate, one probe replicate per array.