Experimental infection workflow. The left udder was challenged by S. aureus whereas the right udder remained uninfected as the control. Then every six hours, milk was sampled and centrifuged to extract RNA from Milk Fat Globule (MFG). At 30 hpi, goats (n = 5) were slaughtered and mammary tissue samples were taken for MEC capture experiments using LCM (total RNA extraction from micro-dissected MEC) and total RNA extraction from deep alveolar mammary parenchyma (referred to as MG). Finally, these different sources of RNA were analyzed using microarrays (only MFG) and qPCR.