S . aureus infection alters global small RNA expression profile in mice mammary tissue in a strain specific manner. (A) Global distribution of small RNA transcripts. Short reads were sequentially mapped to sequences of transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNAs), and microRNA (miRNA) precursor sequences of mouse reference genome. (B) Length distribution of miRNA short reads in all three samples. Reads were adaptor trimmed. Reads <10 nt were discarded and reads >40 nt were shortened to 40 nt by clipping from the 3’ end. (C) Expression heat-map showing the alteration in global miRNA expression in the mice mammary tissue after 24 h of S. aureus infection. Clustering (top) demonstrates that the PBS, SA1, and SA2 samples show complete separation. (D,E) Expression of a set of miRNAs in the SA1 (D) or SA2 (E) Infected mice mammary tissue was analyzed by qRT-PCR. The fold difference in expression of the genes in infected tissue over the PBS control tissue was calculated and plotted as the average of three biological replicates for SA1 and two biological replicates for SA2.