onal annotation aided in the interpretation of our findings. However, annotation of gene function is incomplete selleck inhibitor and this presented some challenges as exem plified by the finding of a skeletal muscle signature in white adipose tissue, which was due to the presence of a related cell type, brown Inhibitors,Modulators,Libraries fat. This study highlights a number of potential biological and technical sources of variation that practitioners should be aware of for both experimental design and interpretation. Much of the between animal variation reported here reflects functions that are sensitive to environmental cues, such as androgen response, circa dian rhythm, and immune response. External environ mental cues tend to elicit similar responses in multiple tissues.

Variation of gene expression within tissues reflects their heterogeneous cellular composition, and is also a major factor contributing to variation in gene expression. This underscores the potential for dissection or biopsy procedures to introduce unwanted variation into studies of gene expression. Adipose tissue is especially problematic in this Inhibitors,Modulators,Libraries regard as it is Inhibitors,Modulators,Libraries a highly dynamic and heterogeneous tissue with few anatomical features to guide consistent dissection. Our tissue collection procedure involved a coarse separation of tissue fragments which, in retrospect, was useful to reveal within tissue heterogeneity. An excep tion to this was our use of the intact left and right kid neys as replicates. This may explain the relatively low within mouse variation observed for this heterogeneous and highly structured tissue.

In future studies, we Inhibitors,Modulators,Libraries recommend the use of procedures that more effectively homogenize tissue, such as pulverization and mixing of snap frozen samples. Our finding also raises questions about the potential for introducing systematic variation in the dissection of anatomical substructures. This may be a particular concern for studies of gene expression in the brain, for which we have no data at this time. The presence of biologically meaningful covariation in a setting with no experimental perturbation underscores the need for replication and careful adherence to statis tical design principles in gene expression studies. See mingly innocuous experimental factors such as co housing of mice can result in systemic differences that may lead to strong statistical support for incorrect con clusions.

Prior knowledge of the categories of genes that are intrinsically variable can help to identify such effects. Our study further demonstrates that the variation used to construct statistical tests in microar ray experiments Drug_discovery can have substantial correlation across large sets of genes. This can have a profound impact on testing procedures, especially those that rely on multiple test adjustment of p values across many genes. Methods Animals and RNA isolation We obtained 12 C57BL 6J male mice from make it clear The Jackson Laboratory. Six pairs of littermates were housed together from weaning and put on LabDiets 5k52 diet in a facility with