Table SI. Genes overexpressed in CD34+CD7+ prothymocytes.

Probe Symbol Description GenBank CD7_EXP_1 CD7_EXP_2 CD10_EXP_1 CD10_EXP_2 DN_EXP1

1553183_at UMODL1 uromodulin-like 1 NM_173568 9.6 9.8 6.7 6.3 7 1553970_s_at CEL carboxyl ester lipase (bile salt-stimulated lipase) BC042510 7.4 8.1 5.2 6 4.9 1555120_at CD96 CD96 molecule BC020749 5.9 6.9 4 5.3 4 1556967_at ZDHHC14 zinc finger, DHHC-type containing 14 BC008978 4.7 4.6 2.8 2.7 3.3 1557534_at LOC339862 hypothetical protein LOC339862 BC035826 5 5.2 1.9 2.4 3.5 1558972_s_at THEMIS thymocyte selection associated BC043608 3.9 4.4 2.3 2 2.1 1568838_at LOC100132169 similar to hCG1742852 AI015847 6 5.6 4.1 3.4 3.5 1569225_a_at SCML4 sex comb on midleg-like 4 (Drosophila) BC021582 6.2 6 4.1 4.4 3.4 201195_s_at SLC7A5 solute carrier family 7 (cationic amino acid transporter, y+ system) member 5 AB018009 10.2 9.9 7.5 7.3 8.9 204529_s_at TOX thymocyte selection-associated high mobility group box AI961231 8.6 8.8 6.8 7.3 6.8 205083_at AOX1 aldehyde oxidase 1 NM_001159 5.8 5.1 4 3.6 4 205291_at IL2RB interleukin 2 receptor, beta NM_000878 8.6 8.2 5.3 4.8 4.9 205330_at MN1 meningioma (disrupted in balanced translocation) 1 NM_002430 10 10.1 6.7 5.4 7.7 205488_at GZMA granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3) NM_006144 7 6.3 3.6 3.9 3.4 205821_at KLRK1 killer cell lectin-like receptor subfamily K, member 1 NM_007360 7.7 7.7 5.2 5.6 5.1 205910_s_at CEL carboxyl ester lipase (bile salt-stimulated lipase) NM_001807 6.3 7 4.4 5.1 4.2 206067_s_at WT1 Wilms tumor 1 NM_024426 6.9 7.7 5.8 5 5.7 206337_at CCR7 chemokine (C-C motif) receptor 7 NM_001838 6.7 6.8 4.8 4.6 5.6 206366_x_at XCL1 chemokine (C motif) ligand 1 U23772 8.6 8 3.9 4.1 3.9 206481_s_at LDB2 LIM domain binding 2 NM_001290 5.5 6 3.6 3.4 3.6 206641_at TNFRSF17 tumor necrosis factor receptor superfamily, member 17 NM_001192 6.5 6.8 3.6 3.5 5.5 206761_at CD96 CD96 molecule NM_005816 8.6 8.9 6 6.9 6.1 killer cell lectin-like receptor subfamily C, member 1 /// killer cell lectin-like 206785_s_at KLRC1 /// KLRC2 NM_002260 6 5.6 2.1 2.4 2.4 receptor subfamily C, member 2 207723_s_at KLRC3 killer cell lectin-like receptor subfamily C, member 3 NM_002261 4.8 4.1 2.7 2.7 2.5 207840_at CD160 CD160 molecule NM_007053 6.5 5.7 3.7 3.2 3.3 209173_at AGR2 anterior gradient homolog 2 (Xenopus laevis) AF088867 4.3 6.1 3.5 3.3 3.7 209604_s_at GATA3 GATA binding protein 3 BC003070 7.3 7.2 4.7 3.9 5.7 209679_s_at SMAGP small cell adhesion glycoprotein BC003379 8.1 8.3 4.8 5.2 6 209982_s_at NRXN2 neurexin 2 AA608820 8.3 8.5 6 6.9 6.3 209983_s_at NRXN2 neurexin 2 AB035266 7.5 7.8 5.2 6.3 6.4 210095_s_at IGFBP3 insulin-like growth factor binding protein 3 M31159 6.1 7 4.8 4.3 5

2

Table SI. Continued.

Probe Symbol Description GenBank CD7_EXP_1 CD7_EXP_2 CD10_EXP_1 CD10_EXP_2 DN_EXP1

210116_at SH2D1A SH2 domain containing 1A AF072930 6.5 6.9 3.4 4.1 3.9 210370_s_at LY9 lymphocyte antigen 9 AF244129 6 6.2 3.3 3.5 4.7 210432_s_at SCN3A sodium channel, voltage-gated, type III, alpha subunit AF225986 8.3 7.8 5.4 5.5 4.9 210915_x_at TRBC1 T cell receptor beta constant 1 M15564 8.8 8.9 6.2 5.6 7.1 211796_s_at TRBC1 T cell receptor beta constant 1 AF043179 9.5 10 7.3 6.5 8.1 213193_x_at TRBC1 T cell receptor beta constant 1 AL559122 9 9 6.3 5.7 7 213830_at TRD@ T cell receptor delta locus AW007751 8.3 8.9 4.5 4.6 4.9 214022_s_at IFITM1 interferon induced transmembrane protein 1 (9-27) AA749101 10.5 10.1 8.9 8 9 214049_x_at CD7 CD7 molecule AI829961 7.7 7.6 4.4 4.4 4.6 214470_at KLRB1 killer cell lectin-like receptor subfamily B, member 1 NM_002258 7.8 7.2 4.4 4.6 4.7 214551_s_at CD7 CD7 molecule NM_006137 5.4 5.6 3.4 3 3.4 214567_s_at XCL1 /// XCL2 chemokine (C motif) ligand 1 /// chemokine (C motif) ligand 2 NM_003175 7.9 7.5 3.3 3.1 3.3 214617_at PRF1 perforin 1 (pore forming protein) AI445650 8.9 8.8 5.5 5.3 6.1 216191_s_at TRA@ /// TRD@ T cell receptor alpha locus /// T cell receptor delta locus X72501 6.5 7.3 2.5 2.6 3.4 217143_s_at TRA@ /// TRD@ T cell receptor alpha locus /// T cell receptor delta locus X06557 8.7 9.3 5.1 4.8 5.7 217623_at MYLK3 myosin light chain kinase 3 BF114815 4.6 4.4 2.8 2.9 2.8 220646_s_at KLRF1 killer cell lectin-like receptor subfamily F, member 1 NM_016523 6 5.4 4 3.9 4.5 220668_s_at DNMT3B DNA (cytosine-5-)-methyltransferase 3 beta NM_006892 9.9 10.6 8.2 8.1 8.5 221075_s_at NCR2 natural cytotoxicity triggering receptor 2 NM_004828 4.7 4.9 3.1 3.1 3.4 223340_at ATL1 atlastin GTPase 1 AF131801 6.1 6.7 4.6 4.8 5.2 223939_at SUCNR1 succinate receptor 1 AF348078 7.5 8.8 3.4 3.7 7 224646_x_at H19 H19, imprinted maternally expressed transcript (non-protein coding) BF569051 5.8 7.3 4.4 4.4 4.5 226311_at BF058422 5.4 4 2.5 2.5 2.7 226682_at RORA RAR-related orphan receptor A AW006185 5.4 5 2.4 2.5 2.7 226982_at ELL2 elongation factor, RNA polymerase II, 2 AI745624 6.2 6.1 3.9 3.6 5 227210_at SFMBT2 Scm-like with four mbt domains 2 T65020 9.2 9.5 7 7 8.2 227449_at EPHA4 EPH receptor A4 AI799018 4.7 5.5 2.5 2.7 3.1 227875_at KLHL13 kelch-like 13 (Drosophila) AB037730 5.9 7 3 2.6 5.2 228599_at MS4A1 membrane-spanning 4-domains, subfamily A, member 1 AI862674 8.4 7.2 6.5 5.6 5 228737_at TOX2 TOX high mobility group box family member 2 AA211909 6.3 5.3 2.9 2.6 4.4 229629_at AI923633 7.5 8.1 5.2 5.6 6

3

Table SI. Continued.

Probe Symbol Description GenBank CD7_EXP_1 CD7_EXP_2 CD10_EXP_1 CD10_EXP_2 DN_EXP1

230233_at BF110534 6.9 6.5 5.2 4.9 5.5 230481_at ACY3 aspartoacylase (aminocyclase) 3 AI393205 6.9 8.2 4.9 5 5 231303_at NCRNA00158 non-protein coding RNA 158 BE672389 4.6 6 3 3.8 3.8 234994_at TMEM200A transmembrane protein 200A AA088177 6.2 6.5 3.6 3.7 4.9 235133_at AI807143 5.1 5.4 3.1 3 4 235343_at VASH2 vasohibin 2 AI961235 6.3 6.2 4.4 4.2 4.6 235816_s_at RGL4 ral guanine nucleotide dissociation stimulator-like 4 AI867408 8.5 8.8 5.5 5.5 6.9 236901_at AA035730 6.5 6.1 3.6 4 3.4 237403_at GFI1B growth factor independent 1B transcription repressor AI097490 7.4 7.3 5 4.4 5.6 240179_at BF112218 5.3 6.5 3.3 2.8 3.3 243040_at AA760776 5.6 5.6 3.4 3.2 4.4

4

Table SII. Genes overexpressed in CD34+CD19+ pro-B cells.

Probe Symbol Description GenBank CD7_EXP_1 CD7_EXP_2 CD10_EXP_1 CD10_EXP_2 DN_EXP1 1553145_at FLJ39653 hypothetical FLJ39653 BC010030 6.4 6.8 8.9 9.3 6.1 1554140_at WDR78 WD repeat domain 78 BC032406 3.8 4.1 5.6 5.8 2.7 1556451_at AL833645 6.2 6 9.2 9.5 5.5 1556598_at ARPP21 cyclic AMP-regulated phosphoprotein, 21 kD AI698023 2.2 2.5 6.7 6.9 2.2 1556599_s_at ARPP21 cyclic AMP-regulated phosphoprotein, 21 kD AI698023 4.4 4.4 8.9 9.3 3.8 1557030_at GAB1 GRB2-associated binding protein 1 BC030751 3.2 3.1 6.7 6.5 3.3 1557706_at ZHX2 zinc fingers and homeoboxes 2 BM677619 4.3 4.5 7.2 7.9 3.6 1559221_at BC040870 3.1 3.2 8.3 8.7 3.5 1559315_s_at LOC144481 hypothetical protein LOC144481 AK054607 5.7 5.4 8.1 7.9 4.4 1559618_at LOC100129447 hypothetical protein LOC100129447 BQ188678 6.2 5.3 9.8 9.2 5 1559864_at LCN6 lipocalin 6 BC040937 6.1 6 8.7 8.6 5 1560018_at ARPP21 cyclic AMP-regulated phosphoprotein, 21 kD H44077 3.6 3.5 8.7 8.7 3.6 1560610_at BU565621 5.2 5.3 8.5 8.9 3.5 1561363_a_at AI419968 3.4 3.1 6.3 6.5 2.8 1563209_a_at MACROD2 MACRO domain containing 2 BC035876 3.9 3.8 7 7 3.3 1563849_at SH2D4B SH2 domain containing 4B AK091518 3.3 3.1 7.2 7.8 2.9 1566362_at DNTT Deoxynucleotidyltransferase, terminal AA585152 7.5 7 9.8 9.8 6.5 1566363_at DNTT deoxynucleotidyltransferase, terminal AA585152 11.7 11.2 13.6 13.5 10.6 1566428_at AL833199 6.1 5.4 8.4 8.1 3.2 1568611_at CA418310 5.8 5 9.5 9.2 4.3 201005_at CD9 CD9 molecule NM_001769 6.7 6.6 12.1 12.4 6.7 202587_s_at AK1 adenylate kinase 1 BC001116 6.3 6.1 8.7 8.8 5.7 202723_s_at FOXO1 forkhead box O1 AW117498 6.5 5.9 9.7 9.6 5 202724_s_at FOXO1 forkhead box O1 NM_002015 7.1 6.4 9.9 9.9 5.2 202733_at P4HA2 prolyl 4-hydroxylase, alpha polypeptide II NM_004199 6.6 6.3 9.9 9.9 4.8 202761_s_at SYNE2 spectrin repeat containing, nuclear envelope 2 NM_015180 5.9 5.4 8.6 8.6 4.4 203066_at CHST15 carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15 NM_014863 9.8 9 11.1 10.7 7.6 203325_s_at COL5A1 collagen, type V, alpha 1 AI130969 6.5 6.2 8.8 8.8 5.9 203354_s_at PSD3 pleckstrin and Sec7 domain containing 3 AW117368 5 4.8 8.1 8.6 4.9 203355_s_at PSD3 pleckstrin and Sec7 domain containing 3 NM_015310 5.8 4.9 9.3 9.7 4.8 203372_s_at SOCS2 suppressor of cytokine signaling 2 AB004903 6.2 6.7 9.3 9.3 6.2

5

Table SII. Continued.

Probe Symbol Description GenBank CD7_EXP_1 CD7_EXP_2 CD10_EXP_1 CD10_EXP_2 DN_EXP1 203434_s_at MME membrane metallo-endopeptidase AI433463 6.5 4.7 10.4 10.4 4.2 203435_s_at MME membrane metallo-endopeptidase NM_007287 6.9 5.4 10.6 10.6 5.2 203504_s_at ABCA1 ATP-binding cassette, sub-family A (ABC1), member 1 NM_005502 4.3 4.9 6.9 7.2 3.3 203505_at ABCA1 ATP-binding cassette, sub-family A (ABC1), member 1 AF285167 5.3 5.6 7.7 8 4.4 203556_at ZHX2 zinc fingers and homeoboxes 2 NM_014943 7.7 7.3 10.6 10.9 6.6 204030_s_at SCHIP1 schwannomin interacting protein 1 NM_014575 7.5 7.6 10.7 10.8 7.6 204114_at NID2 nidogen 2 (osteonidogen) NM_007361 4.5 3.6 9 8 4.4 204684_at NPTX1 neuronal pentraxin I NM_002522 3.8 3.9 8.7 6.2 4.2 204730_at RIMS3 regulating synaptic membrane exocytosis 3 NM_014747 7.3 6.2 9.9 9.7 5.5 205267_at POU2AF1 POU class 2 associating factor 1 NM_006235 10.3 9.7 12 11.9 7.8 205297_s_at CD79B CD79b molecule, immunoglobulin-associated beta NM_000626 9.2 8.7 11.5 11.4 7.3 205352_at SERPINI1 serpin peptidase inhibitor, clade I (neuroserpin), member 1 NM_005025 6 6 7.5 8.5 5 206001_at NPY neuropeptide Y NM_000905 6.6 6.3 8.8 8.2 4.1 206110_at HIST1H3H histone cluster 1, H3h NM_003536 4.4 5.1 7.5 7.6 4.2 206150_at CD27 CD27 molecule NM_001242 5.5 5.2 8.5 9 5.2 206492_at FHIT fragile histidine triad gene NM_002012 6.7 6.7 9.2 9.2 5.9 206591_at RAG1 recombination activating gene 1 NM_000448 7.7 9.1 11 11.4 6.2 206937_at SPTA1 spectrin, alpha, erythrocytic 1 (elliptocytosis 2) NM_003126 5.1 4.5 8.1 7.7 4.6 inhibitor of DNA binding 3, dominant negative helix-loop-helix 207826_s_at ID3 NM_002167 6.5 7.3 9.1 10 6.6 protein 208015_at SMAD1 SMAD family member 1 NM_015583 3.5 4.4 7.2 8 3.7 208302_at HMHB1 histocompatibility (minor) HB-1 NM_021182 5.4 5.3 8.9 9.4 4.1 208650_s_at CD24 CD24 molecule BG327863 7.9 5.9 10.4 10.5 5.9 208651_x_at CD24 CD24 molecule M58664 8.1 6.4 10.6 10.6 6.5 209101_at CTGF connective tissue growth factor M92934 4.4 3.4 8.5 6.8 3.9 209183_s_at C10orf10 chromosome 10 open reading frame 10 AL136653 4.8 4.6 11 11.1 4.3 209398_at HIST1H1C histone cluster 1, H1c BC002649 7.3 7.1 10 10 7 huntingtin interacting protein 1 related /// similar to KIAA0655 209558_s_at HIP1R /// LOC100294412 AB013384 6.5 6.1 8.5 8.4 5.2 protein 209691_s_at DOK4 docking protein 4 BC003541 5.9 6.4 8.2 8.2 5.3 209771_x_at CD24 CD24 molecule AA761181 10.6 8.7 12.8 12.9 8.8 209772_s_at CD24 CD24 molecule X69397 6.5 5.4 9.3 9.4 5.6

6

Table SII. Continued.

Probe Symbol Description GenBank CD7_EXP_1 CD7_EXP_2 CD10_EXP_1 CD10_EXP_2 DN_EXP1 209789_at CORO2B coronin, actin binding protein, 2B BF939649 4.4 2.9 8.1 8.2 3.1 209911_x_at HIST1H2BD histone cluster 1, H2bd BC002842 6.9 7 9.1 9.5 6.3 210387_at HIST1H2BG histone cluster 1, H2bg BC001131 6 6 9.3 9.2 5.3 210450_at LOC90925 hypothetical protein LOC90925 BC002792 5.1 3.8 8.7 8.6 4.6 210487_at DNTT deoxynucleotidyltransferase, terminal M11722 9.2 9.1 12.2 12.4 8.4 210517_s_at AKAP12 A kinase (PRKA) anchor protein 12 AB003476 6.5 4.4 11.8 11.7 5.7 210948_s_at LEF1 lymphoid enhancer-binding factor 1 AF294627 5.7 5.8 7.8 8.5 4.5 210993_s_at SMAD1 SMAD family member 1 U54826 6.7 7.3 9.8 10 6.6 211596_s_at LRIG1 leucine-rich repeats and immunoglobulin-like domains 1 AB050468 5.8 5.5 9.4 9.2 6 212012_at PXDN peroxidasin homolog (Drosophila) BF342851 7.5 7 10.7 10.2 6.9 212013_at PXDN peroxidasin homolog (Drosophila) D86983 6.9 5.9 9.8 9.3 5.9 212488_at COL5A1 collagen, type V, alpha 1 N30339 6.9 6.9 9.3 9.2 6.1 213906_at MYBL1 v-myb myeloblastosis viral oncogene homolog (avian)-like 1 AW592266 5.9 6.1 7.1 7.6 4.4 214373_at AI582773 6.5 6.7 8.2 9.3 5.8 214472_at HIST1H2AD /// HIST1H3D histone cluster 1, H2ad /// histone cluster 1, H3d NM_003530 5.3 5.6 8 7.8 4.2 sema domain, transmembrane domain (TM), and cytoplasmic 215028_at SEMA6A AB002438 5.1 4.7 6.5 6 2.9 domain, (semaphorin) 6A 215071_s_at HIST1H2AC histone cluster 1, H2ac AL353759 6.9 7.5 9.8 10.2 5.6 215117_at RAG2 recombination activating gene 2 AW058148 5.3 6.2 8.3 8.5 2.7 215721_at IGHG1 immunoglobulin heavy constant gamma 1 (G1m marker) X58397 6.5 6.6 8.3 8.3 5 215779_s_at HIST1H2BG histone cluster 1, H2bg BE271470 5.8 6 8.5 8.1 5.4 215925_s_at CD72 CD72 molecule AF283777 7.3 7.5 9.1 9.3 5.7 216080_s_at FADS3 fatty acid desaturase 3 AC004770 5.1 4.2 8.4 8.6 4.9 216379_x_at CD24 CD24 molecule AK000168 10.5 8.7 12.8 12.9 8.7 217402_at AL031732 3.1 3.1 6.3 5.4 2.3 218418_s_at KANK2 KN motif and ankyrin repeat domains 2 NM_015493 6.1 6.6 9.4 9.6 6.3 218613_at PSD3 pleckstrin and Sec7 domain containing 3 NM_018422 4.9 4.4 7.9 8.4 4.3 218625_at NRN1 neuritin 1 NM_016588 3.9 3.8 6.7 6.9 3.9 218829_s_at CHD7 chromodomain helicase DNA binding protein 7 NM_017780 4.5 3.5 7.6 7.6 4.5 219148_at PBK PDZ binding kinase NM_018492 7.5 7.5 9.1 9.1 6.1 219396_s_at NEIL1 nei endonuclease VIII-like 1 (E. coli) NM_024608 6.2 5.4 9.1 8.6 5.6 219522_at FJX1 four jointed box 1 (Drosophila) NM_014344 4.6 4.2 8.1 6.9 4.3

7

Table SII. Continued.

Probe Symbol Description GenBank CD7_EXP_1 CD7_EXP_2 CD10_EXP_1 CD10_EXP_2 DN_EXP1 219840_s_at TCL6 T-cell leukemia/lymphoma 6 AF195820 3.9 3.3 5.9 7.1 3.4 220068_at VPREB3 pre-B lymphocyte 3 NM_013378 9.9 9.4 12.3 12.7 7.2 220359_s_at ARPP21 cyclic AMP-regulated phosphoprotein, 21 kD NM_016300 4.2 4.3 7 6.9 3.3 220450_at NM_024914 4.4 4.8 8.3 9.1 3.9 SPANXB1 /// SPANXB2 /// SPANX family, member B1 /// SPANX family, member B2 /// SPANX 220921_at NM_013453 4.7 3.7 7.8 7.8 3.7 SPANXF1 family, member F1 sperm protein associated with the nucleus, X-linked, family member SPANXA1 /// SPANXA2 /// A1 /// SPANX family, member A2 /// SPANX family, member B1 /// 220922_s_at SPANXB1 /// SPANXB2 /// NM_013453 6.1 4.8 8.3 8.5 5 SPANX family, member B2 /// SPANX family, member C /// SPANX SPANXC /// SPANXF1 family, member F1 221054_s_at TCL6 T-cell leukemia/lymphoma 6 NM_014418 2.8 2.9 6.8 6.6 3.1 221234_s_at BACH2 BTB and CNC homology 1, basic leucine zipper transcription factor 2 NM_021813 7.8 6.5 11 11 6.6 221261_x_at MAGED4 /// MAGED4B melanoma antigen family D, 4 /// melanoma antigen family D, 4B NM_030801 7.3 7.2 8.8 9 6 221349_at VPREB1 pre-B lymphocyte 1 NM_007128 10.4 10.9 12.5 12.6 8.6 221558_s_at LEF1 lymphoid enhancer-binding factor 1 AF288571 10.1 10 12.2 12.4 7.8 221601_s_at FAIM3 Fas apoptotic inhibitory molecule 3 AI084226 7.9 7.3 9.5 9.5 6.2 221909_at RNFT2 ring finger protein, transmembrane 2 AW299700 5.9 5.5 7.9 8.4 5.1 221969_at PAX5 paired box 5 BF510692 10.2 9.2 11.9 11.7 7.9 223313_s_at MAGED4 /// MAGED4B melanoma antigen family D, 4 /// melanoma antigen family D, 4B BC001207 6.2 6.4 8 8.1 5.1 sema domain, transmembrane domain (TM), and cytoplasmic 223449_at SEMA6A AF225425 7 6.3 8.3 7.7 4.9 domain, (semaphorin) 6A 223732_at SLC23A1 solute carrier family 23 (nucleobase transporters), member 1 AF170911 6.5 6.3 7.9 8.4 5.2 224140_at NPCDR1 nasopharyngeal carcinoma, down-regulated 1 AF134979 5.3 5.3 7.7 7.9 4.8 224901_at SCD5 stearoyl-CoA desaturase 5 AL571375 4.6 4.4 6.9 6.9 3.9 225570_at SLC41A1 solute carrier family 41, member 1 AW439816 6.5 6.4 8.5 8.6 5.4 225912_at TP53INP1 tumor protein p53 inducible nuclear protein 1 AW341649 9.2 8 11.3 11 7.6 225998_at GAB1 GRB2-associated binding protein 1 AK022142 6.1 6.6 8.6 9.2 6 226002_at GAB1 GRB2-associated binding protein 1 AK022142 5.9 6.4 8.4 9 5.4 227173_s_at BACH2 BTB and CNC homology 1, basic leucine zipper transcription factor 2 AW450901 7.2 6 9.9 9.8 6.1 227336_at DTX1 deltex homolog 1 (Drosophila) AW576405 6.2 5.5 9.5 9.1 4.7 227529_s_at AKAP12 A kinase (PRKA) anchor protein 12 BF511276 3 2.4 9.5 9.7 2.5 227530_at AKAP12 A kinase (PRKA) anchor protein 12 BF511276 6.1 5.2 11.6 11.7 5.4 227798_at SMAD1 SMAD family member 1 AU146891 7.2 7.2 9.7 9.7 6.5

8

Table SII. Continued.

Probe Symbol Description GenBank CD7_EXP_1 CD7_EXP_2 CD10_EXP_1 CD10_EXP_2 DN_EXP1 229070_at C6orf105 chromosome 6 open reading frame 105 AA470369 3.1 3.2 6.2 7 3.4 229114_at GAB1 GRB2-associated binding protein 1 AW237741 6.7 6.7 9.1 9.6 5.8 229817_at ZNF608 zinc finger protein 608 AI452715 6.8 7.1 8.6 9 5.7 230671_at LOC100288685 Hypothetical protein LOC100288685 BF056222 5.5 5.1 7.8 7.8 4.8 230795_at AI828075 6.5 5.4 8.9 8.5 5.8 231067_s_at AKAP12 A kinase (PRKA) anchor protein 12 BF114967 2.7 2.3 7.5 7.4 2.9 231528_at BE503388 4.9 4.9 7.1 8.3 4.8 231935_at ARPP21 cyclic AMP-regulated phosphoprotein, 21 kD AL133109 5.6 5.8 10.6 10.9 5 232439_at AU145981 5.3 5.4 7.6 7.5 4.4 232882_at AA079839 5.7 5.6 8.7 9 4.3 232951_at AV710143 6.3 6.5 8.9 8.9 5.4 235099_at CMTM8 CKLF-like MARVEL transmembrane domain containing 8 AW080832 7.4 6.7 10.9 10.7 6.1 235175_at GBP4 guanylate binding protein 4 BG260886 6.6 6.5 8.6 8.4 5.5 235278_at MACROD2 MACRO domain containing 2 BF032500 5.5 5.4 8 7.3 4.3 235456_at AI810266 5.3 5.4 8.2 8.7 4.5 236193_at HIST1H2BC histone cluster 1, H2bc AA037483 5.1 4.7 8.6 7.4 4.9 236307_at AA085906 6 5.8 9.1 9.2 5.1 236796_at BACH2 BTB and CNC homology 1, basic leucine zipper transcription factor 2 AI052447 6.5 6.1 9.3 9.7 5.1 237297_at BE675562 4.7 4.3 7.6 8.8 4.7 238071_at LCN10 /// LCN6 lipocalin 10 /// lipocalin 6 AI823802 7.1 7.1 9 9.3 5.7 238297_at AI884781 4.2 5 6.9 7.4 4.1 239214_at LOC100130458 Hypothetical LOC100130458 AA806831 5.8 6.2 8 8.5 4.5 240743_at AW173212 4.1 4.4 6.8 7.6 3.9 240927_at R02287 4.4 5.2 7 8.3 3.8 241679_at AI672553 4 3.9 10.1 10 4.2 243362_s_at LOC641518 hypothetical LOC641518 AA992805 5.2 5.2 8.5 8.6 3.8 243363_at LOC641518 hypothetical LOC641518 AA992805 5.5 5.4 8.9 9.3 5.6 243968_x_at FCRL1 Fc receptor-like 1 AI572979 3.9 3.1 6.3 6.9 3.2 244226_s_at H60543 5.1 4.4 7 7 4.1 244280_at W46364 5 5 10.2 10.1 5 229070_at C6orf105 chromosome 6 open reading frame 105 AA470369 3.1 3.2 6.2 7 3.4

9

Table SII. Continued.

Probe Symbol Description GenBank CD7_EXP_1 CD7_EXP_2 CD10_EXP_1 CD10_EXP_2 DN_EXP1 244868_at AA001941 5.2 4.8 7 7.3 4.1 266_s_at CD24 CD24 molecule L33930 8.8 6.6 11.1 11.1 6.6 huntingtin interacting protein 1 related /// similar to KIAA0655 38340_at HIP1R /// LOC100294412 AB014555 7.7 7.3 9.5 9.4 6.4 protein

Footnote: Results in Tables SI and SII are expressed as fluorescence intensity Log2 values. Comparative analysis of the gene expression profiles of CD34+CD7+ (pro-T), CD34+CD19+ (pro-B) and CD34+Lin- (Imm) HPCs populations was performed with the R package "locfdr" (lfdr < 5%). CD34+CD7+ prothymocytes differentially expressed 73 probe sets corresponding to 64 annotated genes (Table SI). CD34+CD19+ pro-B cells differentially expressed 153 probe sets corresponding to 116 annotated genes (table SII)

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Supplemental Figure Legends

FIGURE S1. Sequential analysis of BM cells and thymocytes from humanized mice.

BM, spleen and thymus cells of irradiated NSG mice injected with UCB CD34+ cells at 2 mo of age were harvested 1M (n=10), 2M (n=10), 3M (n=10) or 5M (n=10) post-graft, and FACS analyzed after labeling with the indicated mAbs. Gates are set on huCD45+ cells. Evolution of (A) BM CD34++CD38low cells or (B) CD4+CD8+ thymocytes. Numbers in quadrant indicate percentages of labeled cells. Data are from one representative mouse out of 10.

FIGURE S2. Effect of BM aging on prothymocyte development and thymus colonization.

UCB CD34+ HPCs were injected into irradiated NSG mice aged 2 (2m), 4 (4m) or 8 (8m) mo (n = 5 of each group). BM or thymus cells were analyzed at 3M post-graft.

(A, B). FACS analysis of (A) BM cells and (B) thymocytes. Cells were labeled with the indicated mAbs; data are shown as dot-plots; numbers in quadrants indicate labeled cell percentages.

(C). Quantification of huCD45+cell populations in the thymus; data are shown as absolute cell numbers (x10-6) or percentages relative to total cells (%); values, and presented as Box and Whiskers plots, thick lines indicating the medians; statistically significant differences (p < 0.05) are marked by asterisks.

(D). Cultures on OP9-DL1 cells. Pro-T2 and CD7lo prothymocytes from the cultures were FACS analyzed at culture d 21. Data are shown as dot-plots or histograms; numbers in quadrants indicate percentages of labeled cells.

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Figure S1 A. 1M 2M 3M 5M

0.9% 0.3% 0.2% 0.1% bone marrow CD34 CD38

B. 1M 2M 3M 5M

15% 4% 5% 90% 15% 77% 88%

71% thymus thymus

5% 3% 2% 3% 0.1% 8% CD4 CD8 A. Figure S2 2m mouse 4m mouse 8m mouse

0.15% 0.1% < 0.05%

CD34 CD7 1.2% 2.0% 1.9%

0.4% 0.3% 0.8%

17% 21% 19% BONE MARROW – 3M CD34 CD38

B. 2m mouse 4m mouse 8m mouse

1.0% 0.4% 0.2% CD34 CD7

6% 88% 8% 86% 4% 91% THYMUS – – 3M THYMUS CD4 CD8 2% 4% 3% 3% 1% 4%

C. D. OP9 – DL1 (day 21) 3 100 )

6 68% 1% 80

2 lo 60 7%

* 40 CD7 DP cells (%) 1 6% 25% cell number (x10 cell number 20

87% 2%

2m 4m 8m 2m 4m 8m

pro-T 7%

8% 3%

CD3 CD5 CD56