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Supplemental Material 1 Supplemental gure 1 Lin-Sca-1- Marker Thymus Bone Skin 41% ±1 64% ±8 92% ±4 CD29 % of max % of max % of max 50% ±10 58% ±9 87% ±4 CD51 % of max % of max % of max 3% ±1 47% ±3 72% ±7 CD140a % of max % of max % of max 39% ±6 51% ±3 71% ±3 CD140b % of max % of max % of max 4% ±2 1% ±1 7% ±1 CD34 % of max % of max % of max 21% ±16 30% ±10 42% ±10 gp38 % of max % of max % of max 50% ±4 43% ±7 55% ±5 Ly51 % of max % of max % of max 49% ±3 8% ±1 73% ±6 CD90.2 % of max % of max % of max 36% ±10 35% ±10 77% ±5 CD105 % of max % of max % of max 2% ±2 47% ±8 78% ±6 CD73 % of max % of max % of max 9% ±8 8% ±3 38% ±2 CD44 % of max % of max % of max 48% ±3 27% ±1 52% ±4 CD146 % of max % of max % of max 17% ±13 11% ±8 28% ±7 Nestin % of max % of max % of max 6% ±5 23% ±29 37% ±25 CXCL12 % of max % of max % of max SUPPLEMENTAL FIGURE 1. Flow cytometry analysis of Lin- Sca-1- cells from the thymus, bone and skin. Overlay histograms illustrate staining with the relevant antibody (in blue) and an isotype control (in red). Each overlay histogram is representative of three independent experiments (3-5 mice per biological replicate). Numbers represent the mean percentage of positive cells (+/- SD). Supplemental gure 2 A B 1000 250k M 100 tMC 98.2% K P bMC 200k R 10 sMC 1 A - 150k 1 9 1 a 4 8 1 0 5 A 2 5 0 3 3 5 9 0 C S CD CD CD gp Ly CD CD1 FSC 100k CD14 CD140b 1000 tMC 50k bMC M 100 sMC K 0 P Thymocytes R 10 -103 0 103 104 105 cTEC 1 mTEC SCA-1 t 5 e 1 m 1 i 4 3 3 n -k ca x c CD CD CD p o E F C tMC vs bMC tMC vs sMC bMC vs sMC 7 7 ) ) ) 6 695 6 6 365 5 426 sMC sMC bMC 5 5 4 4 4 3 3 3 2 2 2 (ReadCount (ReadCount 362 10 10 1 849 1 1 573 log log 0 log10(ReadCount 0 r = 0.476 0 r = 0.629 r = 0.607 0 1 2 3 4 5 6 0 1 2 3 4 5 6 0 1 2 3 4 5 6 log (ReadCount tMC) log10(ReadCount bMC) log10(ReadCount tMC) 10 SUPPLEMENTAL FIGURE 2. Purity of cell populations used for RNA-Seq analyses. (A) Post-sort analysis of sorted Sca-1+ thymic MCs. (B) Upper panel, histogram depicting the expression levels (RPKM) of 10 typical MC markers in the Sca-1+ MCs from the thymus, bone and skin. Lower panel, histogram showing expression levels of genes expressed in thymocytes or TECs. (RPKM = 15; red line) (C) Scatterplots depicting the number of DEGs in each one-to-one comparison of MC populations. Numbers in bold represent the amount of DEGs associated to the respective MC population in each comparison. Pearson correlation value (r) is also depicted in the bottom right corner of each scatterplot. Supplemental figure 3 C1 - Thymus C2 - Bone Z-score Z-score 0 1 2 3 4 5 0 2 4 6 8 quantity of cells (113) quantity of blood cells (82) B migration of cells (145) quantity of leukocytes (77) leukocyte migration (125) cell movement (153) cell movement of lymphocytes (25) cell movement of leukocytes (107) cell movement of cell movement of myeloid cells (77) mononuclear leukocytes (28) Lymphocyte migration (23) cell movement of phagocytes (81) leukocyte migration (48) A cell movement of neutrophils (56) A cell movement of leukocytes (44) recruitment of phagocytes (42) migration of phagocytes (13) chemotaxis of leukocytes (53) migration of antigen presenting cells (10) chemotaxis of phagocytes (45) cell movement of antigen (21) cell movement of presenting cells mononuclear leukocytes (51) migration of phagocytes (37) orientation of cells (8) C infiltration of leukocytes (51) 0 5 10 15 20 infiltration of cells (56) - log P-value ( ) cell movement of antigen (38) 10 presenting cells inflammatory response (95) D C3 - Skin proliferation of cells (183) E Z-score 0 1 2 3 4 angiogenesis (52) vascularization (25) B recruitment of myeloid cells (11) recruitment of cells (14) A internalization of cells (20) F recruitment of phagocytes (11) activation of myeloid cells (31) 2.4 2.6 2.8 3.0 3.2 3.4 C activation of neutrophils (12) - log10 P-value ( ) 0 10 20 30 40 50 ( ) - log10 P-value C4 - Thymus + Bone C6 - Bone + Skin Z-score Z-score 0 5 10 15 0 5 10 15 size of body (27) differentiation of connective (21) B tissue cells B differentiation of cells (58) proliferation of cells (75) C transcription of DNA (29) development of (34) activation of DNA (26) C cardiovascular system endogenous promoter vasculogenesis (27) A angiogenesis (30) fertility (13) E 0 2 4 6 cell viability (21) - log10 P-value ( ) F vasculogenesis (22) D angiogenesis (25) C5 - Thymus + Skin Z-score cell movement (45) 0 2 4 6 cell movement of myeloid cells (22) cell movement of phagocytes (18) migration of cells (20) A cell movement of cell movement of granulocytes (13) myeloid cells (8) A migration of myeloid cells (9) cell movement (8) of phagocytes migration of granulocytes (7) size of body (13) B development of body axis (33) G quantity of cells (21) C proliferation of epithelial cells (17) H differentiation of cells (30) D adhesion of immune cells (10) I 2.0 2.5 3.0 3.5 4.0 0 1 2 3 4 - log10 P-value ( ) - log10 P-value ( ) SUPPLEMENTAL FIGURE 3. Core biological functions associated to the 6 DEG clusters. All functions depicted in histograms were signifcantly enriched (p < 0.05) and activated (Z-score > 2). Related functions were clustered (letters). Numbers in parentheses represent the number of genes per biological functions. Red/black dots represent p-values. Supplemental table 1 # Gene symbol Gene name # Gene symbol Gene name 1 1700048O20Rik RIKEN cDNA 1700048O20 gene 40 Ccl7 chemokine (C-C motif) ligand 7, MCP3 2 2610524H06Rik RIKEN cDNA 2610524H06 gene 41 Cd248 CD248 antigen, endosialin 3 4930452B06Rik RIKEN cDNA 4930452B06 gene 42 Cdk18 cyclin-dePendent kinase 18 4 A4galt alPha 1,4-galactosyltransferase 43 Cdkn1c cyclin-dePendent kinase inhibitor 1C; P57KiP2 5 Acpl2 acid PhosPhatase-like 2 44 Cdkn2b cyclin-dePendent kinase inhibitor 2B (P15, inhibits CDK4) 6 Adam12 a disintegrin and metalloPePtidase domain 12 (meltrin alPha) 45 Cdyl2 chromodomain Protein, Y chromosome-like 2 7 Adam19 a disintegrin and metalloPePtidase domain 19 (meltrin beta) 46 Cep170b centrosomal Protein of 170 kDa Protein B 8 Adam8 a disintegrin and metalloPePtidase domain 8 47 Chst1 carbohydrate (keratan sulfate Gal-6) sulfotransferase 1 a disintegrin-like and metalloPePtidase (reProlysin tyPe) with 9 Adamts12 48 Chst2 carbohydrate sulfotransferase 2 thrombosPondin tyPe 1 motif, 12 a disintegrin-like and metalloPePtidase (reProlysin tyPe) with 10 Adamts2 49 Cib2 calcium and integrin binding family member 2 thrombosPondin tyPe 1 motif, 2 11 Adcy3 adenylate cyclase 3 50 Cldn1 claudin 1 aminoglycoside PhosPhotransferase domain-containing 12 Agphd1 51 Col1a1 collagen, tyPe I, alPha 1 Protein 1 13 Ahr aryl hydrocarbon recePtor 52 Col1a2 collagen, tyPe I, alPha 2 14 Akap2 a-kinase anchor Protein 2 53 Col3a1 collagen, tyPe III, alPha 1 15 Akap6 akap6 Protein 54 Col4a6 collagen, tyPe IV, alPha 6 alkaline PhosPhatase, tissue-nonsPecific isozyme; alkaline 16 Alpl 55 Col6a2 collagen, tyPe VI, alPha 2 PhosPhatase, liver/bone/kidney 17 Angel1 Protein angel homolog 1 56 Coro2a coronin-2A 18 Angptl4 angioPoietin-like 4 57 Crabp1 cellular retinoic acid binding Protein I 19 Aoc3 amine oxidase, coPPer containing 3 58 Creb3l1 cAMP resPonsive element binding Protein 3-like 1 20 Arc activity-regulated cytoskeleton-associated Protein 59 Crip2 cysteine rich Protein 2, CRP-2 21 Arhgap28 rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 60 Csgalnact1 chondroitin sulfate N-acetylgalactosaminyltransferase 1 22 Arhgef28 rho-guanine nucleotide exchange factor 61 Ctsh cathePsin H 23 Arhgef6 rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 62 Ctso cathePsin O 24 Arrb1 beta-arrestin-1 63 Cxcl12 chemokine (C-X-C motif) ligand 12 25 Atp10a ATPase, class V, tyPe 10A 64 Cyp26b1 cytochrome P450, family 26, subfamily b, PolyPePtide 1 UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, 26 B3galnt1 65 Cyp2j6 cytochrome P450 2J6 PolyPePtide 1 27 B4galnt1 beta-1,4 N-acetylgalactosaminyltransferase 1 66 Dclk2 serine/threonine-Protein kinase DCLK2 28 Bach2 transcriPtion regulator Protein BACH2 67 Depdc7 DEP domain containing 7 29 Bmper BMP-binding endothelial regulator Protein 68 Dhrs7 dehydrogenase/reductase (SDR family) member 7 30 Btbd2 Protein Btbd2 69 Dock3 dedicator of cyto-kinesis 3 31 Cables1 CDK5 and Abl enzyme substrate 1 70 Dpysl3 dihydroPyrimidinase-related Protein 3 32 Calcrl calcitonin recePtor-like 71 Dtx3l deltex 3-like (DrosoPhila) 33 Capn6 calPain 6 72 Duoxa1 dual oxidase maturation factor 1 34 Car13 carbonic anhydrase 13 73 Dynap Protein Dynap 35 Car5b carbonic anhydrase 5b, mitochondrial 74 E130311K13Rik RIKEN cDNA E130311K13 gene 36 Casp12 casPase 12 75 Ebf3 early B cell factor 3 37 Cbr2 carbonyl reductase 2 76 Eda ectodysPlasin-A 38 Ccdc80 coiled-coil domain containing 80 77 Efna5 ephrin A5 39 Ccl5 chemokine (C-C motif) ligand 5, RANTES 78 Ehd3 EH-domain containing 3 # Gene symbol Gene name # Gene symbol Gene name eukaryotic translation initiation factor 2C, 4, Protein 79 Eif2c4 120 Il18rap interleukin 18 receptor accessory protein argonaute-4 80 Eif4e3 eukaryotic translation initiation factor 4E member 3 121 Il1r1 interleukin 1 receptor, type I 81 Elfn1 leucine rich repeat and fibronectin type III, extracellular 1 122 Il1rl1 interleukin 1 receptor-like 1 82 Ell2 elongation factor RNA polymerase II 2 123 Il4ra interleukin 4 receptor, alpha 83 Emb embigin 124 Inf2 inverted formin-2 84 En1 homeobox protein engrailed-1 125 Inpp4b inositol polyphosphate-4-phosphatase, type II 85 Epn3 epsin 3 126 Itgb3bp centromere protein R 86 Eya4 eyes absent 4 homolog (Drosophila) 127 Itm2a integral membrane protein 2A 87 Fabp4 fatty acid-binding protein, adipocyte 128 Ivd isovaleryl
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