Germ-free versus conventional mouse terminal ileum

Transcriptomics (using DNA microarrays) was used to quantitatively compare the terminal ileum from conventional and germ-free mice (female and male; C57BL/10A and BALB/c strains). A reference-free experimental design was used. Each 2-color microarray was used to analyze one germ-free and one conventional sample (sex- and strain-matched). To mitigate label-effects, half of the samples of each experimental class were randomly selected to be labeled green, and the other half red. The experiment used 19 microarrays: four female C57BL/10A, five female BALB/c, five male C57BL/10A, and five male BALB/c. All of the microarrays were the same design (design number 017138, Agilent Technologies, Santa Clara, CA).