Guiry et al. BMC Genomics 2010, 11:211 http://www.biomedcentral.com/1471-2164/11/211 Page 4 of 18 A B NP3 P3 PB1 PB2 P1 NP2 NPB1 NPB2 NP1 P2 Figure 2 Hybridisation designs for testes and brain microarray. (a) Testes sample pools were hybridised using a loop design. Three precocious pools (P1-P3) each of four individuals were hybridised to three non-precocious pools (NP1-NP3) each of ten individuals. Each sample pool at the tail of the arrow (green) was Cy3-labelled and that at the arrowhead (red) was Cy5-labelled. Each pool was hybridised three times and at least once with each of the Cy5 or Cy3 dyes to maintain dye balance. Analysis was with LIMMA software. (b) Brain samples were hybridised directly using pools of five individuals. Pool labelling was as detailed above. Two separate pools of precocious brains (PB1 and PB2) were each compared directly to two separate pools of non-precocious brains (NPB1 and NPB2). All hybridisations include dye swaps. Analysis was with LIMMA software. influencing the overall precocious versus non-precocious comparison. From Table 1 it would appear that the protein transla- tional machinery has been substantially down-regulated in precocious males: genes for the heat shock proteins (Hsp70a and Hsp90b), the elongation factors (EF-1alpha, EF-1gamma and EF-2) and the ribosomal proteins (RpL5, RpL8 and RpS5) attest to this. Cathepsin B was up-regulated in the maturing testes as too was an antileukoproteinase similar to trout ovulatory protein (OVP-2): this suggests regulated re-structuring of the gonad in a similar manner to what happens in the ovary. Apolipoprotein (Apo) E is involved in lipoprotein uptake and processing; it is a carrier for lipid into the cells and subsequently mediates the exchange of lipids and cholesterol in LDL. Lipoprotein lipase (Lpl), which digests plasma lipoproteins releasing lipids which apoli- poproteins including ApoE can internalize [25], was also