Table 1.

Stem/progenitor cluster 1 (cryptorchid > wild-type, busulfan-treated; 88 probe sets)

Row	Probe set	Accession no.	Gene	Description
1	98783_at	Y15131	Rbmy1a1	RNA binding motif protein, Y chromosome
2	102627_at	AF061569	Igf2bp1	Insulin-like growth factor 2 mRNA binding protein
3	95063_at	AI606257	Cdca7	Cell division cycle associated 7
4	98108_at	X15789	Crabp1	Cellular retinoic acid binding protein I
5	92290_at	Z19580	Siah1b	Seven in absentia 1B
6	101883_s_at	L22977	Xlr3a /// Xlr3b	X-linked lymphocyte-regulated 3A /// X-linked
7	92607_at	AF017994	Mest	Mesoderm specific transcript
8	161787_f_at	AV363418	Cdt1	Chromatin licensing and DNA replication factor
9	93397_at	U56819	Ccr2	Chemokine (C-C motif) receptor 2
10	94743_f_at	M29009	LOC214403	Complement factor H-related protein
11	100479_at	AA756653	Dnmt3a	DNA methyltransferase 3A
12	96169_at	AA683788	Sall4	Sal-like 4 (Drosophila)
13	92208_at	AI152966	C1qdc1	C1q domain containing 1
14	160702_at	AA791885	Rbm35a	RNA binding motif protein 35A
15	103301_i_at	AA866668	Sox3	SRY-box containing gene 3
16	101853_f_at	M12660	Cfh	Complement component factor h
17	94761_at	X70058	Ccl7	Chemokine (C-C motif) ligand 7
18	161968_f_at	AV370035	Ccr5	Chemokine (C-C motif) receptor 5
19	104116_at	AW124049	D5Ertd593e	DNA segment, Chr 5, ERATO Doi 593, exp
20	93112_at	D86725	Mcm2	Minichromosome maintenance deficient 2 rr
21	104576_at	AW212397	Ski	Sloan-Kettering viral oncogene homolog
22	96047_at	U63146	Rbp4	Retinol binding protein 4, plasma
23	101160_at	X53798	Cxcl2	Chemokine (C-X-C motif) ligand 2
24	100325_at	M65027	Gp49a	Glycoprotein 49 A
25	92291_f_at	M29008	Cfhr1	Complement factor H-related 1
26	97444_at	AI844520	Ifi30	Interferon gamma inducible protein 30
27	93028_at	X58196	H19	H19 fetal liver mRNA
28	102710_at	AF020313	Apbb1ip	Amyloid beta (A4) precursor protein-binding
29	97356_at	AI839653	1810008O21F	RIKEN cDNA 1810008O21 gene
30	104680_at	AJ250489	Ramp1	Receptor (calcitonin) activity modifying protein
31	161984_f_at	AV234303	Col3a1	Procollagen, type III, alpha 1
32	161698_f_at	AV232762	Rprc1	Arginine/proline rich coiled-coil 1
33	100397_at	AF024637	Tyrobp	TYRO protein tyrosine kinase binding protein
34	98817_at	Z29532	Fst	Follistatin
35	94982_f_at	AI852470	Nme3	Expressed in non-metastatic cells 3
36	103033_at	X06454	C4b /// C4a ///	Complement component 4B (Childo blood g
37	103075_at	M34381	Pou5f1	POU domain, class 5, transcription factor 1
38	162483_f_at	AV112006	Col18a1	Procollagen, type XVIII, alpha 1
39	101019_at	U74683	Ctsc	Cathepsin C
40	103981_at	AI842281	U2af1-rs2	U2 small nuclear ribonucleoprotein auxiliary
41	97487_at	X70296	Serpine2	Serine (or cysteine) peptidase inhibitor, clad
42	104237_at	AI838071	Pcbd2	Pterin 4 alpha carbinolamine dehydratase/di
43	93538_at	AW228036	Ttrap	Traf and Tnf receptor associated protein
44	104337_f_at	AW208938	Pkp2	Plakophilin 2
45	104156_r_at	U19118	Atf3	Activating transcription factor 3
46	93041_at	D26089	Mcm4	Minichromosome maintenance deficient 4 h
47	103534_at	V00722	Hbb-b2	Hemoglobin, beta adult minor chain
48	103081_at	AA863928	Baz1b	Bromodomain adjacent to zinc finger domain
49	96083_s_at	AI226368	Hnrpdl	Heterogeneous nuclear ribonucleoprotein D−
50	103449_at	AA795923	Lsm14b	LSM14 homolog B (SCD6, Saccharomyces cerevisiae)
51	98092_at	AA790307	Plac8	Placenta-specific 8
52	96886_at	AW060556	Stab1	Stabilin 1
53	160458_at	AI853261	Mcam	Melanoma cell adhesion molecule
54	95627_at	AW046038	Wwtr1	WW domain containing transcription regulat
55	96891_at	AI842771	Anp32b /// LO	Acidic nuclear phosphoprotein 32 family, me
56	97750_at	X06406	Rpsa	Ribosomal protein SA
57	94954_at	AI846628	Anapc4	Anaphase promoting complex subunit 4
58	103016_s_at	X68273	Cd68	CD68 antigen
59	96138_at	AA682129	Mars	Methionine-tRNA synthetase
60	97199_at	AI854767	Rbm12 /// Cpn	RNA binding motif protein 12 /// copine I
61	95641_at	AI853899	Plac9	Placenta specific 9
62	98624_at	X75316	Rnpc1	RNA-binding region (RNP1, RRM) containin
63	99475_at	U88327	Socs2	Suppressor of cytokine signaling 2
64	98059_s_at	D49733	Lmna	Lamin A
65	98088_at	X13333	Cd14	CD14 antigen
66	95791_s_at	U14648	Sfrs2	Splicing factor, arginine/serine-rich 2 (SC-35
67	104524_at	AI842825	Gltp	Glycolipid transfer protein
68	92794_f_at	M35970	Nme1	Expressed in non-metastatic cells 1, protein
69	103916_at	AI850713	8430420C20F	RIKEN cDNA 8430420C20 gene
70	95944_at	AV299153	Dhx36	DEAH (Asp-Glu-Ala-His) box polypeptide 36
71	100468_g_at	X57687	Lyl1	Lymphoblastomic leukemia
72	94839_at	M96823	Nucb1	Nucleobindin 1
73	98346_at	AI593759	Lrrc54	Leucine-rich repeat containing 54
74	100957_at	AA881160	Ssbp1	Single-stranded DNA binding protein 1
75	94024_at	AA671429	Cdt1	Chromatin licensing and DNA replication factor
76	160182_at	AI846595	Sfrs6	Splicing factor, arginine/serine-rich 6
77	100732_at	X73829	Rps8	Ribosomal protein S8
78	98934_at	AI847513	0610007P06R	RIKEN cDNA 0610007P06 gene
79	93089_at	X12507	Eif4a2	Eukaryotic translation initiation factor 4A2
80	103312_f_at	AW047929	2610101J03R	RIKEN cDNA 2610101J03 gene
81	95657_f_at	AW125164	D13Wsu177e	DNA segment, Chr 13, Wayne State University
82	96710_at	AI854262	H2afv	H2A histone family, member V
83	104573_at	AA921069	Bola2	BolA-like 2 (E. coli)
84	99336_at	U78085	Rps5	Ribosomal protein S5
85	99093_at	AI852864	Rps10 /// LOC	Ribosomal protein S10 /// similar to ribosomal
86	94767_at	U93864	Rps11 /// LOC	Ribosomal protein S11 /// similar to ribosomal
87	101129_at	X83590	Rpl5	Ribosomal protein L5
88	93092_at	U35323	H2-DMa	Histocompatibility 2, class II, locus DMa

Supplemental online Table 3 indicates overlap between stem/progenitor cluster 1 candidate genes (this table), stem/progenitor cluster 2, hematopoietic, neural, and embryonic stem cells and undifferentiated spermatogonia.