Comparison of Rostral and Caudal murine neocortex at E13.5

Rostral and caudal thirds of E13.5 neocortex are compared in both inbred (C57) and oubred (MF1) mice. Keywords: Tissue comparison Two different strains of mice, one inbred (C57Bl\6), the other outbred (MF1), were used to control for strain-dependent variations in patterns of gene expression (Pavlidis and Noble, 2001; Sandberg et al., 2000). For each strain at each timepoint, three sets of pooled rostral and caudal tissue were collected from single litters. Gene expression screens were carried out within single litters to match embryos by developmental age as closely as possible. Individual pools contained material from the left and right cortices of at least two embryos, to correct for variation among dissections. Given the limited amount of RNA available when using such a screening strategy, the corresponding cDNA was amplified using the SMART system to generate enough material for synthesising array probes (Matz et al., 1999), as used successfully for our previous studies (Livesey et al., 2000; Livesey et al., 2004).