Identification of SSC genes and markers in pre-pubertal type A spermatogonia. (A) Rat Affymetrix probe set IDs for ES, PGC, gonocyte and SSC markers were selected and analyzed for expression in the Spga cell fractions at 9 and 22 dpp. Genes up-regulated or down-regulated at least 2 fold in type A Spga (G9) compared to mitotic germ cells at 22 dpp (G22) are shown in the first two columns. Genes with a detectable or undetectable expression in the two last columns (defined here as the number of Affymetrix Present/Absent in the replicates after MAS 5.0 analysis). (B) The 255 rat SSC-specific transcripts identified in a microarray analysis by Hamra et al.  were compared to each respective gene cluster defined in Figure 2B. Left: Shown are the number of transcripts in each cluster (e.g. G9 vs G22) which overlapped with the transcript list by Hamra et al.  as compared to the number of randomly expected transcripts (64/17; i.e. 64 observed versus 17 expected in a random distribution). The gradual color code bar shows over-representation (red) and under-representation (blue) of SSC specific gene transcripts described by Hamra et al.  in the various clusters defined in this study (Figure 2B). Significance of overlap (p Values) was calculated using a Gaussian hypergeometric test (Fischer exact probability test). Right: Gene list and functional classification of the genes up-regulated in mitotic Spga type A at 9 dpp overlapping with the rat SSC cluster predicted by Hamra et al .