This study investigated the role of local genetic variation on gene expression. To this end, gene expression variation between strains isolated from two locations (Orsay and Santeuil) was investigated by microarray. As an outgroup the N2, CB4856, WN2001, WN2002, WN2003, JU314 and JU396 were used. Age-synchronized strains were grown for 47 hours at 20 degrees Celsius, where after strains were sampled and RNA was isolated. Labelled cRNA was hybridized to microarray to assess the impact of local genetic variation on gene expression. DNA hybridization complementing this study can be found in E-MTAB-8126.