Supplementary Materials

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1 Supplementary Materials Supplemental figure 1. Absolute cell count of naïve/memory compartment of CD4 and CD8 T cells in early years Absolute cell number of naïve (CD45RA+CCR7+), Stem cell memory T cell (Tscm, CD45RA+CCR7+CD28+CD27+FAS+), central memory (Tcm, CD45RA- CCR7+), effector memory (Tem, CD45RA- CCR7- ), and Temra (effector memory re- expressing CD45RA, CD45RA+CCR7+) T cells respectively (young HC, n=9-10, black circles; young Tx, n=10, gray circles) A) For CD4 T cells, B) CD8 T cells. median shown. Statistical difference is indicated with * for P<0.05, Mann- Whitney U test used.

2 Supplemental figure 2. Thymic regeneration occurs in the majority of children and restores the naïve T cell compartment A) Absolute cell number of CD3+, CD4+ and CD8+ T cells (lymphocytes x 10^9/L) in neonatally thymectomized children, aged 10 years or older, divided by high CD31 expression (gray squares, n=17) and low CD31 expression (open squares, n=7). B) Absolute cell number of naïve (CD45RA+CCR7+), Tscm (Stem cell memory T cell, CD45RA+CCR7+CD28+CD27+FAS+), central memory (Tcm, CD45RA- CCR7+), effector memory (Tem, CD45RA- CCR7- ), and Temra (effector memory re- expressing CD45RA, CD45RA+CCR7+) for CD4+ T cells respectively. C) Absolute numbers of CD8 naïve, Tscm, Tem, Tcm and Temra respectively. D) Percentages of CD8 naïve, Tscm, Tem, Tcm, Temra respectively. (HC>10yr, n=10, black squares; Tx>10yr, n=24, gray squares; Tx>10yr low CD31, open gray squares) Median depicted. Statistical difference is indicated with * for P<0.05, Mann- Whitney U test used.

3 Supplemental figure 3. CD4+ naïve T cells of young thymectomized children show lower calcium flux and IL- 8 intensity, but have similar calcium flux capacity as healthy children. A) Left panel, Calcium flux of HC>10yr (older HC) naïve CD4+ (black line, n=4) and CD4+ memory (gray line, n=4); Right panel, AUC of paired calcium flux of naïve and memory CD4+ T cells. B) Maximum calcium flux after stimulation with ionomycin (HC 1-5yr, n=4; Tx 1-5yr, n=6). Statistical difference is indicated with * for P<0.05, Mann- Whitney U test used.

4 Supplemental figure 4. CD31- naïve CD4+ T cells have increased IFNγ production IFNγ production of CD31+ and CD31- naïve CD4+ T cells in young healthy and thymectomized children. (HC 1-5yr, n=14, black circles; Tx1-5yr, n=15, gray circles). Statistical difference is indicated with * for P<0.05, Mann- Whitney U test used for unpaired data and Wilcoxon signed rank test for paired data

5 Supplemental figure 5. Production of IL- 8 by CD31+ naïve CD4+ is correlated to PTK7 A) Representative histogram of IL- 8 production in PTK7+ (black line) and PTK7- (gray) CD31+ naïve CD4+ T cells. Geo mean of PTK7 expression in IL- 8 negative (gray) and IL- 8 positive (black) CD31+ naïve CD4+ T cells (n=5; HC 1-5yr). B) representative FACSplot of PTK7 expression of each cell division after cytokine stimulation. C) representative FACSplot of IL- 8 expression of each cell division after cytokine stimulation. D) combined data set for corresponding percentages of IL- 8 and PTK7 per patient and division (n=4; HC1-5yr) E) representative FACSplot of CD31 expression after cytokine stimulation per cell division. Right panel, summary of mean fluorescence intensity (MFI) of CD31 per cell division after cytokine stimulation (n=6; HC>10yr). F) left panel, representative FACSplot of IFNγ expression after cytokine stimulation per cell division. Right panel, summary of IFNγ percentage per cell division after cytokine stimulation (n=6; HC>10yr). Statistical difference is indicated with * for P<0.05, Wilcoxon signed rank test for paired data

6 Supplemental figure 6. Representative FACS gating strategy for sorting of CD31+ naive CD4+ T cells. Single cell lymphocytes were gated on CD3+ and CD4+ expression (1 st panel), followed by exclusion of CD25+CD127- (Treg) cells (non- Treg, 2 nd panel), selection of CD31+CD45RA+ expression (3 rd panel), and further exclusion of CD45RO+ and CCR7- T cells to exclude possible Temra or CD45RA+CD45RO+ double positive T cells contamination (non- Temra, 4 th panel)

7 Supplemental figure 7. Pathway enrichment analysis for CD31+ naïve T cells of Tx 1-5yr and HC 1-5yr. A) Description of significant pathways that are differentially expressed between CD31+ naïve CD4+ T cells of Tx1-5yr (n=4) and HC1-5yr (n=3). B) Description of pathways upregulated in CD31+ naïve CD4+ T cells of Tx1-5yr (n=4) in comparison to HC1-5yr (n=3). Significance determined by FDR (B&H) p- value.

8 Supplemental table 1. Differential gene expression between CD31+ naïve CD4+ T cells of thymectomized and healthy children. Gene name Refseq id Base Mean log2foldchange p- value p- value adjusted GBP5 NM_ , , ,31901E- 18 2,94496E- 14 BHLHE40 NM_ , , ,64317E- 18 2,94496E- 14 GBP5 NM_ , , ,37768E- 17 8,14943E- 14 EDA NM_ , , ,69756E- 16 2,3771E- 12 EDA NM_ , , ,69756E- 16 2,3771E- 12 TOX NM_ , , ,22234E- 15 3,61527E- 12 MYO15B NR_ , , ,5154E- 15 6,3769E- 12 PTGER2 NM_ , , ,91551E- 13 1,09038E- 09 PREX1 NM_ , , ,57843E- 13 1,69148E- 09 AFF2 NM_ , , ,09039E- 12 9,03341E- 09 RICS NM_ , , ,92632E- 10 6,33423E- 07 FAM101B NM_ , , ,50437E- 10 1,29742E- 06 ISM1 NM_ , , ,83679E- 10 1,29742E- 06 SUSD4 NM_ , , ,62934E- 09 3,33287E- 06 TIMP1 NM_ , , ,11067E- 09 4,8632E- 06 RICS NM_ , , ,61642E- 09 5,12019E- 06 CACNA1I NM_ , , ,58998E- 08 2,55344E- 05 CACNA1I NM_ , , ,58998E- 08 2,55344E- 05 HES4 NM_ , , ,48062E- 08 3,19725E- 05 HES4 NM_ , , ,60334E- 08 3,19725E- 05 PYHIN1 NM_ , , ,36155E- 08 3,51818E- 05 PYHIN1 NM_ , , ,36155E- 08 3,51818E- 05 PLXDC1 NM_ , , ,56066E- 08 6,60511E- 05 RAB15 NM_ , , ,0371E- 07 7,37388E- 05 SCRN1 NM_ , , ,03881E- 07 7,37388E- 05 TTC28 NM_ , , ,08174E- 07 7,38329E- 05 ENO1 NM_ , , ,70381E- 07 0, HDGFRP3 NM_ , , ,62199E- 07 0, STMN1 NM_ , , ,60945E- 07 0, STMN1 NM_ , , ,60945E- 07 0, STMN1 NM_ , , ,60945E- 07 0,

9 SLC40A1 NM_ , , ,86228E- 07 0, TRIM32 NM_ , , ,59059E- 07 0, TRIM32 NM_ , , ,59059E- 07 0, EDARADD NM_ , , ,41268E- 07 0, NPAS2 NM_ , , ,38705E- 07 0, EDARADD NM_ , , ,41268E- 07 0, GGT1 NM_ , , ,7316E- 07 0, TIMP2 NM_ , , ,78859E- 07 0, GGT1 NM_ , , ,84562E- 07 0, FLNB NM_ , , ,47648E- 07 0, FLNB NM_ , , ,5911E- 07 0, SNHG3 NR_ , , ,80958E- 07 0, FLNB NM_ , , ,47648E- 07 0, FLNB NM_ , , ,5911E- 07 0, GGT1 NM_ , , ,51955E- 07 0, GZMK NM_ , , ,39043E- 07 0, GGT1 NM_ , , ,51955E- 07 0, MT2A NM_ , , ,23163E- 07 0, TCF12 NM_ , , ,93308E- 07 0, TCF12 NM_ , , ,93308E- 07 0, TCF12 NM_ , , ,93308E- 07 0, TCF12 NM_ , , ,93308E- 07 0, FLJ40330 NR_ , , ,61281E- 07 0, STAT4 NM_ , , ,71544E- 07 0, NIN NM_ , , ,93085E- 07 0, CYB561 NM_ , , ,00554E- 06 0, CYB561 NM_ , , ,00554E- 06 0, CYB561 NM_ , , ,00291E- 06 0, ZC3H12D NM_ , , ,13055E- 06 0, NIN NM_ , , ,20456E- 06 0, LSR NM_ , , ,23148E- 06 0, TCF12 NM_ , , ,29194E- 06 0, LSR NM_ , , ,41593E- 06 0, LSR NM_ , , ,42313E- 06 0,

10 SNHG5 NR_ , , ,57707E- 06 0, ADAMTSL5 NM_ , , ,65242E- 06 0, PYHIN1 NM_ , , ,88629E- 06 0, PYHIN1 NM_ , , ,88629E- 06 0, FXYD5 NR_ , , ,99153E- 06 0, FXYD5 NM_ , , ,04134E- 06 0, SCRN1 NM_ , , ,05653E- 06 0, FXYD5 NM_ , , ,11089E- 06 0, FXYD5 NM_ , , ,1153E- 06 0, IGF2R NM_ , , ,33385E- 06 0, SCRN1 NM_ , , ,29672E- 06 0, SCRN1 NM_ , , ,31514E- 06 0, IFITM1 NM_ , , ,94191E- 06 0, FAM195A NM_ , , ,37359E- 06 0, NIN NM_ , , ,58213E- 06 0, LETMD1 NM_ , , ,98676E- 06 0, LETMD1 NM_ , , ,27019E- 06 0, AOAH NM_ , , ,32227E- 06 0, CAPN2 NM_ , , ,52588E- 06 0, CAPN2 NM_ , , ,97574E- 06 0, SH3PXD2A NM_ , , ,24195E- 06 0, SERTAD2 NM_ , , ,79765E- 06 0, DYNLT1 NM_ , , ,01473E- 06 0, APP NM_ , , ,65354E- 06 0, GRIP1 NM_ , , ,0021E- 06 0, HERC1 NM_ , , ,62094E- 06 0, OBSCN NM_ , , ,9033E- 06 0, SLFN13 NM_ , , ,1636E- 06 0, CCDC59 NM_ , , ,66053E- 06 0, SOCS2 NM_ , , ,02186E- 05 0, CA6 NM_ , , ,23101E- 05 0, TOB1 NM_ , , ,29345E- 05 0, APP NM_ , , ,47894E- 05 0, GSTK1 NM_ , , ,53021E- 05 0,

11 TMPRSS3 NR_ , , ,5221E- 05 0, MRC2 NM_ , , ,90555E- 05 0, EPHB6 NM_ , , ,96894E- 05 0, ACCN2 NM_ , , ,03631E- 05 0, ACCN2 NM_ , , ,03631E- 05 0, RNF157 NM_ , , ,00869E- 05 0, TET1 NM_ , , ,17071E- 05 0, APP NM_ , , ,30355E- 05 0, AK1 NM_ , , ,44242E- 05 0, AKAP11 NM_ , , ,47539E- 05 0, TBK1 NM_ , , ,57832E- 05 0, FAM113B NM_ , , ,88917E- 05 0, GAPDH NM_ , , ,9891E- 05 0, HIGD2A NM_ , , ,97574E- 05 0, C8orf59 NM_ , , ,23065E- 05 0, GZMA NM_ , , ,57034E- 05 0, GALNT6 NM_ , , ,55162E- 05 0, C8orf59 NM_ , , ,5128E- 05 0, CAMSAP1L1 NM_ , , ,74657E- 05 0, LY86 NM_ , , ,05315E- 05 0, C5orf13 NM_ , , ,33403E- 05 0, C5orf13 NM_ , , ,245E- 05 0, ANKRD50 NM_ , , ,90519E- 05 0, C5orf13 NM_ , , ,245E- 05 0, C5orf13 NM_ , , ,245E- 05 0, GSTK1 NM_ , , ,33091E- 05 0, TYMP NM_ , , ,88121E- 05 0, C5orf13 NM_ , , ,245E- 05 0, C5orf13 NM_ , , ,245E- 05 0, C8orf59 NM_ , , ,2249E- 05 0, TYMP NM_ , , ,86509E- 05 0, C5orf13 NM_ , , ,245E- 05 0, FOSL2 NM_ , , ,20691E- 05 0, C5orf13 NM_ , , ,33403E- 05 0,

12 C5orf13 NM_ , , ,245E- 05 0, C5orf13 NM_ , , ,07552E- 05 0, C5orf13 NM_ , , ,245E- 05 0, C8orf59 NM_ , , ,47794E- 05 0, SLC35F2 NM_ , , ,49722E- 05 0, TYMP NM_ , , ,45817E- 05 0, APP NM_ , , ,58782E- 05 0, ETS1 NM_ , , ,84558E- 05 0, APP NM_ , , ,96493E- 05 0, ZBTB34 NM_ , , ,12508E- 05 0, RELB NM_ , , ,14297E- 05 0, NHEDC2 NM_ , , ,23906E- 05 0, PSME2 NM_ , , ,31564E- 05 0, GSTK1 NM_ , , ,32027E- 05 0, SNHG1 NR_ , , ,35931E- 05 0, SUSD4 NM_ , , ,84287E- 05 0, ETS1 NM_ , , ,8841E- 05 0, IRS1 NM_ , , ,96524E- 05 0, RCN3 NM_ , , ,21042E- 05 0, SARDH NM_ , , ,44734E- 05 0, SARDH NM_ , , ,44734E- 05 0, VGLL4 NM_ , , ,90658E- 05 0, ACTN1 NM_ , , ,98053E- 05 0, GSTK1 NM_ , , ,33883E- 05 0, HMBOX1 NM_ , , ,3357E- 05 0, ETS1 NM_ , , ,51918E- 05 0, IFITM2 NM_ , , ,59871E- 05 0, YARS NM_ , , ,67056E- 05 0, S100A4 NM_ , , ,96106E- 05 0, PASK NM_ , , ,89663E- 05 0, S100A4 NM_ , , ,96106E- 05 0, ACTN1 NM_ , , ,94999E- 05 0, CERKL NM_ , , ,36694E- 05 0, CERKL NM_ , , ,36694E- 05 0,

13 CERKL NR_ , , ,36694E- 05 0, CERKL NM_ , , ,36694E- 05 0, CERKL NM_ , , ,36694E- 05 0, CERKL NM_ , , ,36694E- 05 0, CERKL NR_ , , ,36694E- 05 0, LDHA NM_ , , ,59064E- 05 0, REST NM_ , , ,11163E- 05 0, ACTN1 NM_ , , ,27091E- 05 0, RPLP1 NM_ , , ,328E- 05 0, OXA1L NM_ , , ,42157E- 05 0, RPLP1 NM_ , , ,53683E- 05 0, ACVR1 NM_ , , ,6995E- 05 0, ACVR1 NM_ , , ,67864E- 05 0, SLU7 NM_ , , ,8286E- 05 0, LDHA NR_ , , ,86006E- 05 0, OBSCN NM_ , , , , SH3BGRL3 NM_ , , , , BCOR NM_ , , , , SRGN NM_ , , , , BCOR NM_ , , , , MTHFD2 NR_ , , , , HMBOX1 NM_ , , , , BCOR NM_ , , , , BCOR NM_ , , , , MTHFD2 NM_ , , , , RGS12 NM_ , , , , NUAK2 NM_ , , , , EIF2C3 NM_ , , , , MDGA1 NM_ , , , , NFKBIZ NM_ , , , , IL16 NM_ , , , , RAPGEF6 NM_ , , , , CHMP7 NM_ , , , , SLCO3A1 NM_ , , , ,

14 IL16 NM_ , , , , FKBP11 NM_ , , , , NFKBIZ NM_ , , , , MDFIC NM_ , , , , MDFIC NM_ , , , , STXBP1 NM_ , , , , STXBP1 NM_ , , , , LDHA NM_ , , , , ISG15 NM_ , , , , LDHA NM_ , , , , CHD9 NM_ , , , , CBL NM_ , , , , RNF41 NM_ , , , , RNF41 NM_ , , , , ODC1 NM_ , , , , FLJ43663 NR_ , , , , B2M NM_ , , , , RNF41 NM_ , , , , LGALS9 NM_ , , , , LDHA NM_ , , , , C17orf49 NM_ , , , , ZC3H12A NM_ , , , , IL21R NM_ , , , , BCL9 NM_ , , , , S100A10 NM_ , , , , C17orf49 NM_ , , , , MARCKSL1 NM_ , , , , NR3C1 NM_ , , , , RWDD1 NM_ , , , , TGFBR2 NM_ , , , , CD40LG NM_ , , , , RWDD1 NM_ , , , , LGALS9 NR_ , , , , OASL NM_ , , , ,

15 SNX6 NM_ , , , , SNX6 NM_ , , , , UPP1 NM_ , , , , CREM NM_ , , , , NBL1 NM_ , , , , CREM NM_ , , , , NBL1 NM_ , , , , CREM NM_ , , , , CREM NM_ , , , , CREM NM_ , , , , SBDS NM_ , , , , RWDD1 NM_ , , , , YBX1 NM_ ,7143 0, , , CHST2 NM_ , , , , TLR2 NM_ , , , , SULT1B1 NM_ , , , , FRY NM_ , , , , TJP3 NM_ , , , , NHP2 NM_ , , , , CLEC2B NM_ , , , , FBXO11 NM_ , , , , TGFBR2 NM_ , , , , BCL11A NM_ , , , , LGALS9 NM_ , , , , SYN1 NM_ , , , , SON NM_ , , , , LSM7 NM_ , , , , SYN1 NM_ , , , , NME2P1 NR_ , , , , FLJ43663 NR_ , , , , PDE7A NM_ , , , , KLF11 NM_ , , , , NCRNA00164 NR_ , , , , UPP1 NM_ , , , ,

16 WHAMM NM_ , , , , APOL3 NR_ , , , , DEGS1 NM_ , , , , ATF4 NM_ , , , , APOL3 NR_ , , , , DCHS1 NM_ , , , , MRPS21 NM_ , , , , VGLL4 NM_ , , , , SON NM_ , , , , CREM NM_ , , , , C7orf50 NM_ , , , , C7orf50 NM_ , , , , C7orf50 NM_ , , , , ZBP1 NM_ , , , , PRDX6 NM_ , , , , SIPA1L3 NM_ , , , , MRPS21 NM_ , , , , FOXO1 NM_ , , , , RPLP0 NM_ , , , , ODZ1 NM_ , , , , RPLP0 NM_ , , , , ODZ1 NM_ , , , , ODZ1 NM_ , , , , LZTFL1 NM_ , , , , ACVR2B NM_ , , , , ZNF696 NM_ , , , , MYBL1 NM_ , , , , CD97 NM_ , , , , MYBL1 NM_ , , , , IL21R NM_ , , , , OASL NM_ , , , , STRN NM_ , , , , NFATC1 NM_ , , , , CD97 NM_ , , , ,

17 DDB2 NM_ , , , , CCDC85B NM_ , , , , EIF5A NM_ , , , , EIF5A NM_ , , , , EIF5A NM_ , , , , ARHGAP26 NM_ , , , , ARHGAP26 NM_ , , , , C8orf45 NM_ , , , , EIF5A NM_ , , , , TSC22D2 NM_ , , , , APOL3 NM_ , , , , APOL3 NM_ , , , , EIF2C3 NM_ , , , , APOL3 NM_ , , , , CD97 NM_ , , , , STMN1 NM_ , , , , SNRPG NM_ , , , , HMBS NM_ , , , , NME2 NM_ , , , , ADAMTS10 NM_ , , , , TNF NM_ , , , , HPCAL4 NM_ , , , , APPL1 NM_ , , , , NME2 NM_ , , , , NME2 NM_ , , , , ABHD2 NM_ , , , , PELI1 NM_ , , , , ABHD2 NM_ , , , , NME2 NM_ , , , , ATF4 NM_ , , , , SLCO3A1 NM_ , , , , GPR132 NM_ , , , , SCAI NM_ , , , , APOL3 NR_ , , , ,

18 NRGN NM_ , , , , VIPR1 NM_ , , , , NRGN NM_ , , , , PLSCR3 NM_ , , , , LOC NM_ , , , , RARRES3 NM_ , , , , IL21R NM_ , , , , CTSW NM_ , , , , EMP3 NM_ , , , , TTC16 NM_ , , , , SCAI NM_ , , , , GADD45B NM_ , , , , PLEKHG2 NM_ , , , , ANKRD44 NM_ , , , , LY6E NM_ , , , , LY6E NM_ , , , , KLF13 NM_ , , , , HMBS NM_ , , , , RGS12 NM_ , , , , LDOC1L NM_ , , , , ZNF792 NM_ , , , , FKBP11 NM_ , , , , DRAP1 NM_ , , , , FAM13A NM_ , , , , MAN1A2 NM_ , , , , BAT2L NM_ , , , , NME1- NME2 NM_ , , , , NDUFV2 NM_ , , , , FAM13A NM_ , , , , CD109 NM_ , , , , GUK1 NM_ , , , , C17orf49 NM_ , , , , TAF4B NM_ , , , , EPSTI1 NM_ , , , ,

19 EPSTI1 NM_ , , , , ZNF394 NM_ , , , , DPP4 NM_ , , , , VGLL4 NM_ , , , , UQCRFS1 NM_ , , , , IDI1 NM_ , , , , GUK1 NM_ , , , , TTC39C NR_ , , , , NT5C3 NM_ , , , , CBR3 NM_ , , , , MAN2C1 NM_ , , , , TP53TG1 NR_ , , , , CTDSP2 NM_ , , , , SEL1L3 NM_ , , , , LBH NM_ , , , , NT5C3 NR_ , , , , GBP2 NM_ , , , , ZBP1 NM_ , , , , CSTB NM_ , , , , GTF3A NM_ , , , , FTH1 NM_ , , , , B4GALT3 NM_ , , , , IFITM3 NM_ , , , , MAPKAPK3 NM_ , , , , NT5C3 NM_ , , , , SLC39A8 NM_ , , , , H1FX NM_ , , , , RAB25 NM_ , , , , CD109 NM_ , , , , MSH2 NM_ , , , , NT5C3 NM_ , , , , NR3C1 NM_ , , , , NR3C1 NM_ , , , , CSDAP1 NR_ , , , ,

20 C19orf70 NM_ , , , , LTA NM_ , , , , VGLL4 NM_ , , , , FNBP1 NM_ , , , , TNFRSF10B NR_ , , , , PVT1 NR_ , , , , TNFRSF1B NM_ , , , , CLIC1 NM_ , , , , SYF2 NM_ , , , , ZBP1 NM_ , , , , NR3C1 NM_ , , , , EMR4P NR_ , , , , PPA2 NM_ , , , , HINT1 NR_ , , , , NR3C1 NM_ , , , , RPL39 NM_ , , , , EPPK1 NM_ , , , , NR3C1 NM_ , , , , MAP1LC3A NM_ , , , , LDHA NM_ ,4828 0, , , NR3C1 NM_ , , , , GPRC5B NM_ , , , , LBXCOR1 NM_ , , , , LOC NR_ , , , , BTLA NM_ , , , , CREM NM_ , , , , GUK1 NM_ , , , , CCNL1 NM_ , , , , OSGIN1 NM_ , , , , OSGIN1 NM_ , , , , PIK3CG NM_ , , , , IL17RA NM_ , , , , C10orf35 NM_ , , , , RAG1AP1 NM_ , , , ,

21 TXNL1 NR_ , , , , TMPRSS3 NM_ , , , , ADCY9 NM_ , , , , TNFRSF10B NM_ , , , , UHMK1 NM_ , , , , PELI2 NM_ , , , , CREM NM_ , , , , NDUFA7 NM_ , , , , ARID1A NM_ , , , , ANKK1 NM_ , , , , RAB4B NM_ , , , , GOLGA7B NM_ , , , , TXNL1 NM_ , , , , ACVR1C NM_ , , , , NHP2 NM_ , , , , SLC39A8 NM_ , , , , LOC NR_ , , , , MAN2A1 NM_ , , , , CDGAP NM_ , , , , BOLA2 NM_ , , , , ZC3HAV1 NM_ , , , , BOLA2B NM_ , , , , RPS29 NM_ , , , , P2RY11 NM_ , , , , SEMA4D NM_ , , , , CREM NM_ , , , , KIAA1432 NM_ , , , , ERC1 NR_ , , , , ARID1A NM_ , , , , RPL28 NM_ , , , , RPL28 NM_ ,6698 0, , , ZBTB44 NM_ , , , , USP10 NM_ , , , , SYNE2 NM_ , , , ,

22 BCL3 NM_ , , , , LAMP3 NM_ , , , , RPL41 NM_ , , , , ZNF445 NM_ , , , , RAG1AP1 NM_ , , , , ODF3B NM_ , , , , HCST NM_ , , , , BTLA NM_ , , , , HCST NM_ , , , , ACVR1C NM_ , , , , COX7A2 NR_ , , , , SSNA1 NM_ , , , , TP53INP2 NM_ , , , , NFKBIA NM_ , , , , ACVR1C NM_ , , , , LTA NM_ , , , , RPL41 NM_ , , , , CUX1 NM_ , , , , RAG1AP1 NM_ , , , , ERC1 NR_ , , , , THOC4 NM_ , , , , OSGIN1 NM_ , , , , RABGGTB NM_ , , , , ERC1 NM_ , , , , MAP3K7IP2 NM_ , , , ,

23 Supplemental table 2. Differential gene expression between CD31+ and CD31- naïve CD4+ T cells of thymectomized children Gene name Refseq id Base Mean log2foldchange p- value p- value adjusted PECAM1 NM_ , , ,32149E- 17 7,66832 E- 13 MAF NM_ , , ,9188E- 09 9,14107 E- 05 FAM129C NM_ , , ,52509E- 08 0, MAF NM_ , , ,05523E- 06 0,

24 Supplemental table 3. Differential gene expression between CD31+ and CD31- naïve CD4+ T cells of healthy children Gene name Refseq id Base Mean log2foldchange p- value p- value adjusted PECAM1 NM_ ,3161 2, ,59E- 30 4,83E- 26 PYHIN1 NM_ ,9948-1, ,62E- 09 3,56E- 05 PYHIN1 NM_ ,9948-1, ,62E- 09 3,56E- 05 PASK NM_ ,527-1, ,65E- 09 3,56E- 05 MAF NM_ ,5755-1, ,07E- 08 4,01E- 05 TOX2 NM_ ,0959 1, ,42E- 08 5,02E- 05 TOX2 NM_ ,5652 1, ,41E- 08 5,02E- 05 TOX2 NM_ ,0959 1, ,42E- 08 5,02E- 05 TOX2 NM_ ,0959 1, ,42E- 08 5,02E- 05 PLXND1 NM_ ,7822 1, ,3E- 08 5,45E- 05 SYK NM_ , , ,97E- 08 5,45E- 05 SYK NR_ , , ,97E- 08 5,45E- 05 SYK NM_ , , ,09E- 08 5,45E- 05 SYK NR_ , , ,09E- 08 5,45E- 05 FLJ40330 NR_ ,1594 1, ,21E- 08 0, FAM101B NM_ ,485 0,7369 1,04E- 07 0, GBP5 NM_ ,3008-1, ,75E- 07 0, PREX1 NM_ ,745-0, ,02E- 07 0, GBP5 NM_ ,047-1, ,78E- 07 0, PYHIN1 NM_ ,2576-1, ,29E- 06 0, PYHIN1 NM_ ,2576-1, ,29E- 06 0, GBP2 NM_ ,085-0, ,78E- 06 0, IKZF2 NM_ ,5382 0, ,65E- 06 0, CD8B NM_ , , ,43E- 06 0, CD8B NM_ , , ,43E- 06 0, MIAT NR_ ,0661-1, ,84E- 06 0, CD8B NM_ , , ,92E- 05 0, FRY NM_ ,3923 0, E- 05 0, FXYD5 NR_ ,535-0, ,7E- 05 0, CD8B NM_ , , ,54E- 05 0, FXYD5 NM_ ,313-0, ,58E- 05 0, UHMK1 NM_ ,1406 0, ,31E- 05 0,014848

25 FXYD5 NM_ ,345-0, ,59E- 05 0, FXYD5 NM_ ,839-0,6223 2,64E- 05 0, LRRN3 NM_ ,823 0, ,86E- 05 0, LRRN3 NM_ ,583 0, ,02E- 05 0, CD8B NM_ , , ,68E- 05 0, CAMK4 NM_ ,337 0, ,63E- 05 0, FCRL2 NM_ ,6392 0, ,86E- 05 0, LRRN3 NM_ ,041 0, ,87E- 05 0, F5 NM_ ,4492-0, ,54E- 05 0, LSR NM_ ,2851-0, ,8E- 05 0, LSR NM_ ,5957-0, ,63E- 05 0, LSR NM_ ,34-0, ,89E- 05 0, KCNA3 NM_ ,57 0, ,67E- 05 0, RHOH NM_ ,377 0, ,57E- 05 0,038839

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