Table 2.
Comparative gene expression among stem cells and spermatogonia
| Stem/progenitor cluster 2 (Cr > Bu) SSC (389)a | Cultured SSCs (4,889)b | Type A spermatogonia (6,102)c | HSC (2,598)d | NSC (3,036)d | ESC (2,176)d | |
|---|---|---|---|---|---|---|
| No. of probe setse | 389 | 275 | 352 | 110 | 147 | 147 |
| Expectedf | – | 184 | 191 | 81 | 95 | 68 |
| Probability (p)g | – | <1.0 × 10−15 | <1.0 × 10−16 | <0.0003 | 1.9 × 10−9 | 3.3 × 10−16 |
In the current study, Affymetrix mouse genome U74Av2 arrays containing 12,422 probe sets were used to evaluate gene expression in Cr, wild-type, and Bu testis.
Supplemental online Table 3 gives a complete list of genes in stem/progenitor cluster 2, indicating where each gene overlaps with gene lists for HSCs, NSCs, ESCs, SSCs, and type A spermatogonia. Overlap with stem/progenitor cluster 1 is also indicated in supplemental online Table 3.
Oatley et al. [31] used Affymetrix MG340 2.0 arrays to evaluate gene expression in cultured SSCs. MGU74Av2 contains 8975 best matches with MG340 2.0, and 4,889 of these were expressed by cultured SSCs.
Shima et al. [30] used Affymetrix MGU74Av2 arrays (same arrays used in the current study) to identify 6,102 genes expressed by isolated type A spermatogonia.
Ivanova et al. [1] and Ramalho-Santo et al. [2] characterized and compared gene expression in three different stem cell populations. The stem cell candidate gene lists from these two studies were merged to create composite gene lists for HSCs, NSCs, and ESCs. Both studies used Affymetrix MGU74Av2 arrays.
Number of probe sets that overlap with stem/progenitor cluster 2 (Cr > Bu) candidate SSC gene list generated in the current study.
Hypergeometric distribution was used to determine the level of overlap between candidate gene lists expected by chance. For example, the type A spermatogonia list contains 6,102 candidate probe sets, which comprise 49% (6,102 of 12,422) of probe sets on the mouse MGU74Av2 array. Therefore, 49% (191) of the 389 stem/progenitor cluster 2 probe sets are expected to overlap with the Shima et al. [30] list by chance.
The probability (p) that the level of overlap observed is different from that expected by chance.
Abbreviations: Bu, busulfan-treated; Cr, cryptorchid; ESC, embryonic stem cell; HSC, hematopoietic stem cell; NSC, neural stem cell; SSC, spermatogonial stem cell.