Data analysis of the miRNA microarray.

<p>Total RNA was isolated from gonocytes and spermatogonia (three biological replicates) and analysed using the Illumina mouse miRNA microarray (version 1 revision 2). A) Significance Analysis of Microarrays (SAM) statistical software output (academic version 2.23 <a href="http://www-stat.stanford.edu/_tibs/SAM/" target="_blank">http://www-stat.stanford.edu/_tibs/SAM/</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035553#pone.0035553-Tusher1" target="_blank">[44]</a> was used to identify significantly different miRNA molecules between gonocytes and spermatogonia. SAM expression analysis was performed with a two-class unpaired Wilcoxon test on unlogged data using 500 permutations. Significant miRNA species had a q-value<4 (false discovery rate <4%). Seven miRNA molecules were identified by SAM; 3 were up-regulated in spermatogonia (red) while 4 were down-regulated (green). B) The expression of the significant miRNAs in the individual replicates used for the array was examined using a heat map (Java Treeview) red staining indicating higher expression. miRs 136, 743a and 463* were expressed at consistently higher levels in the spermatogonia samples and the expression of miRs 293, 291a-5p, 294* and 290-5p were expressed at consistently lower levels in spermatogonia.