Supplementary Figure S1. Results of flow cytometry analysis, performed to estimate CD34 positivity, after immunomagnetic separation in two different experiments. As monoclonal antibody for labeling the sample, the fluorescein isothiocyanate (FITC)- conjugated mouse anti-human CD34 MoAb (Mylteni) was used. Briefly, cell samples were incubated in the presence of the indicated MoAbs, at the proper dilution, in PBS containing 5% FCS and 1% Fc receptor (FcR) blocking reagent (Miltenyi) for 30 min at 4 C. Cells were then washed twice, resuspended with PBS and analyzed by a Coulter Epics XL (Coulter Electronics Inc., Hialeah, FL, USA) flow cytometer.

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1 Supplementary Table S1. Complete list of the datasets used in this study and their sources.

GEO Total samples Geo selected GEO accession of used Platform Reference series in series samples samples

GSM142565 GSM142566 GSM142567

GSM142568 GSE6146 HG-U133A 14 8 - GSM142569

GSM142571 GSM142572 GSM142574

GSM51391

GSM51392 GSE2666 HG-U133A 36 4 1 GSM51393

GSM51394

only GSM321583 GSE12803 HG-U133A 20 3 GSM321584 2 GSM321585 use

Promyelocytes_1 Promyelocytes_2 Promyelocytes_3

Promyelocytes_4 HG-U133A 8 8 3 GSE64282 Promyelocytes_5

Promyelocytes_6 Promyelocytes_7 Promyelocytes_8

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2 Supplementary Table S2. Chromosomal regions up-regulated in CD34+ samples as identified by the LAP procedure with the two-class statistics coded in the PREDA R package and an FDR threshold of 0.5. Functional enrichment analysis has been performed using DAVID (http://david.abcc.ncifcrf.gov/) and Gene Ontology (GO) Biological Process annotations have been considered statistically significant if the p- value of the Fisher Exact test was ≤ 0.001 (Benjamini correction).

Chromosome Start End Genes Enriched GO categories FSHR; NRXN1; GPR75; PSME4; ACYP2; 49285481 58427447 RPL23AP32; SPTBN1; RTN4; MTIF2; CCDC88A; EFEMP1; VRK2; FANCL ASNSD1; OSGEPL1; PMS1; MSTN; HIBCH; 2 --- INPP1; MFSD6; NAB1; GLS; STAT1; STAT4; 190530840 198842016 MYO1B; OBFC2A; SDPR; DNAH7; STK17B; GTF3C3; PGAP1; SF3B1; COQ10B; HSPE1; PHOCN; PLCL1 ALCAM; CBLB; BBX; CD47; IFT57; HHLA2; 105190728 108173692 MYH15 SENP2; TRA2B; ETV5; DGKG; TBCCD1; AHSG; FETUB; HRG; KNG1; EIF4A2; RFC4; ADIPOQ; ST6GAL1; RPL39L; MASP1; RTP4; SST; BCL6; LPP; TP63; LEPREL1; CLDN1; 3 --- CLDN16; IL1RAP; FGF12; MGC2889; 185326457 197679885 HRASLS; OPA1; HES1; CPN2; LRRC15; GP5; ATP13A3; LSG1; ACAP2; PPP1R2; APOD; only MUC4; TNK2; TFRC; PCYT1A; UBXN7; PAK2; SENP5; NCBP2; PIGZ; MFI2; DLG1; BDH1; KIAA0226; IQCG; RPL35A PCDH7; ARAP2; C4orf19; PTTG2; TBC1D1; FLJ13197; KLF3; TLR1; TLR6; FAM114A1; use TMEM156; WDR19; RFC1; LIAS; UGDH; UBE2K; PDS5A; RHOH; CHRNA9; RBM47; 4 30935230 48640848 --- APBB2; UCHL1; LIMCH1; PHOX2B; TMEM33; SLC30A9; ATP8A1; GUF1; GABRA2; GABRA4; GABRB1; COMMD8; ATP10D; CORIN; CNGA1; TXK; TEC; FRYL E2F3; CDKAL1; CD24; SOX4; PRL; MRS2; GPLD1; ALDH5A1; KIAA0319; TDP2; DNA packaging; nucleosome ACOT13; C6orf62; GMNN; FAM65B; assembly; chromatin assembly; CMAHP; LRRC16A; SCGN; SLC17A4; protein-DNA complex assembly; SLC17A1; SLC17A3; SLC17A2; TRIM38; nucleosome organization; HIST1H1A; HIST1H3A; HIST1H4A; chromatin assembly or HIST1H4B; HIST1H3B; HIST1H2AB; disassembly; macromolecular HIST1H2BB; HIST1H3C; HIST1H1C; HFE; complex assembly; 6 20448041 27219950 HIST1H4C; HIST1H1E; HIST1H2BD; macromolecular complex subunit HIST1H2BE; HIST1H4D; HIST1H3D; organization; chromatin HIST1H2BF; HIST1H4E; HIST1H2BG; organization; cellular HIST1H2AE; HIST1H1D; HIST1H4F; macromolecular complex Non-commercialHIST1H4G; HIST1H3F; HIST1H2BH; assembly; cellular HIST1H3G; HIST1H2BI; HIST1H4H; macromolecular complex subunit BTN3A2; BTN2A2; BTN3A1; BTN3A3; organization; chromosome BTN2A1; BTN1A1; HMGN4; ABT1; organization HIST1H2BK; PRSS16 MEOX2; SOSTDC1; ANKMY2; BZW2; TSPAN13; AGR2; AHR; SNX13; PRPS1L1; 15688573 23558029 HDAC9; TWIST1; TWISTNB; ITGB8; SP4; RAPGEF5; STEAP1B; IL6; TOMM7; KLHL7; NUPL2; GPNMB; IGF2BP3; TRA2A LRRN3; DOCK4; ZNF277; IFRD1; 7 --- TMEM168; GPR85; PPP1R3A; MDFIC; TFEC; TES; CAV2; CAV1; MET; CAPZA2; 110748284 123588372 ST7; WNT2; CFTR; NAA38; ANKRD7; KCND2; TSPAN12; ING3; C7orf58; WNT16; PTPRZ1; AASS; CADPS2; TAS2R16; SLC13A1; NDUFA5; WASL; HYAL4; SPAM1 PTPRD; TYRP1; MPDZ; NFIB; CER1; SNAPC3; PSIP1; BNC2; CNTLN; SH3GL2; 9463485 19648021 9 RRAGA; HAUS6; PLIN2; DENND4C; RPS6; --- SLC24A2 101260922 102702866 GABBR2; GALNT12; COL15A1; TGFBR1;

3 SEC61B; NR4A3; STX17 MAP3K8; ZEB1; ARHGAP12; KIF5B; 30736813 35928769 C10orf68; NRP1; PARD3; CUL2; CREM; FZD8 ACSL5; ZDHHC6; TCF7L2; HABP2; NRAP; 10 --- CASP7; DCLRE1A; ADRB1; C10orf118; 114161026 119305506 TDRD1; ABLIM1; ATRNL1; GFRA1; PNLIP; PNLIPRP1; PNLIPRP2; HSPA12A; KIAA1598; SLC18A2; EMX2 PRB4; PRB1; ETV6; BCL2L14; LRP6; MANSC1; CREBL2; GPR19; CDKN1B; APOLD1; DDX47; GPRC5A; GPRC5D; 12 11461691 16731165 HEBP1; HTR7P1; KIAA1467; GSG1; EMP1; --- GRIN2B; ATF7IP; PLBD1; GUCY2C; H2AFJ; WBP11; ART4; MGP; ARHGDIB; PDE6H; PTPRO; EPS8; STRAP; DERA; LMO3 FRS2; CCT2; CNOT2; KCNMB4; PTPRB; PTPRR; TSPAN8; LGR5; ZFC3H1; RAB21; TBC1D15; TRHDE; ATXN7L3B; GLIPR1; KRR1; PHLDA1; NAP1L1; BBS10; OSBPL8; ZDHHC17; CSRP2; NAV3; SYT1; PAWR; 69918845 92536863 PPP1R12A; MYF6; MYF5; LIN7A; ACSS3; PPFIA2; CCDC59; SLC6A15; ALX1; RASSF9; NTS; C12orf29; CEP290; KITLG; DUSP6; GALNT4; ATP2B1; EPYC; KERA; LUM; DCN; BTG1 IGF1R; SYNM; TTC23; MEF2A; ASB7; 15 99350259 101937160 --- ALDH1A3; LRRK1; CHSY1; PCSK6 RIOK3; C18orf8; NPC1; LAMA3; CABYR; only 18 21047942 24438863 OSBPL1A; IMPACT; HRH4; SS18; TAF4B; --- AQP4 NDUFA13; LPAR2; GMIP; ATP13A1; ZNF14; ZNF253; ZNF93; ZNF682; ZNF85; 19633016 23852863 use ZNF430; ZNF493; ZNF43; ZNF208; ZNF257; ZNF91; ZNF675 ZNF667; ZNF471; ZIM2; PEG3; USP29; ZNF264; AURKC; ZNF460; ZNF304; Regulation of transcription, DNA- ZNF548; ZNF749; VN1R1; ZNF419; dependent; regulation of RNA 19 ZNF549; ZNF134; ZNF211; ZNF551; metabolic process; regulation of ZNF154; ZNF671; ZNF586; ZNF552; transcription; transcription 56969732 59091264 ZNF587; ZNF606; ZNF135; ZSCAN18; ZNF329; ZNF274; ZNF544; ZNF8; ZNF132; ZNF324B; ZNF324; ZNF446; SLC27A5; TRIM28; CHMP2A; UBE2M; MZF1; MGC2752 BMP2; HAO1; TMX4; PLCB1; PLCB4; 20 6754827 9668862 --- C20orf103; PAK7

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4 Table S3. Chromosomal regions up-regulated in CD14- samples as identified by the LAP procedure with the two-class statistics coded in the PREDA R package and an FDR threshold of 0.5. Functional enrichment analysis has been performed using DAVID (http://david.abcc.ncifcrf.gov/) and Gene Ontology (GO) Biological Process categories. GO annotations have been considered statistically significant if the p-value of the Fisher Exact test was ≤ 0.001 (Benjamini correction).

Chromosome Start End Genes Enriched GO categories KIF3C; HADHA; HADHB; OTOF; KCNK3; C2orf18; CENPA; MAPRE3; TMEM214; AGBL5; EMILIN1; KHK; CGREF1; PREB; SLC5A6; C2orf28; CAD; SLC30A3; UCN; MPV17; GTF3C2; EIF2B4; SNX17; PPM1G; 2 26177449 31777848 --- NRBP1; FNDC4; GCKR; CCDC121; GPN1; SUPT7L; MRPL33; RBKS; BRE; FOSL2; PPP1CB; TRMT61B; WDR43; CLIP4; ALK; YPEL5; LBH; GALNT14; EHD3; XDH; SRD5A2 HPGD; GLRA3; ADAM29; GPM6A; SPCS3; VEGFC; NEIL3; AGA; ODZ3; DCTD; WWC2; 4 175427686 185711982 --- CDKN2AIP; ING2; C4orf41; IRF2; CASP3; MLF1IP; ACSL1 PDGFA; PRKAR1B; HEATR2; SUN1; ADAP1; CYP2W1; GPER; MICALL2; INTS1; MAFK; 548190 2825851 MAD1L1; FTSJ2; NUDT1; EIF3B; CHST12; only LFNG; IQCE; GNA12 7 --- NSUN5; FKBP6; FZD9; BAZ1B; BCL7B; TBL2; MLXIPL; WBSCR22; STX1A; ABHD11; 72719689 74123525 CLDN3; CLDN4; ELN; LIMK1; LAT2; RFC2; CLIP2; GTF2IRD1; GTF2I use MCPH1; ANGPT2; AGPAT5; DEFB1; 8 6382626 9526650 Defense response DEFA6; DEFA4; DEFA5; MFHAS1; TNKS UBAC1; LHX3; DKFZP434A062; CARD9; SNAPC4; SDCCAG3; PMPCA; INPP5E; SEC16A; NOTCH1; EGFL7; AGPAT2; C9orf86; EDF1; TRAF2; C8G; PTGDS; CLIC3; 9 138839021 141058224 --- ABCA2; FUT7; NPDC1; ENTPD2; UAP1L1; MAN1B1; GRIN1; ANAPC2; SSNA1; NDOR1; RNF208; TUBB2C; COBRA1; C9orf167; NELF; EHMT1; CACNA1B; TUBBP5 GHITM; CDHR1; LRIT1; RGR; FAM190B; 85906248 89288720 WAPAL; LDB3; BMPR1A; MMRN2; SNCG; C10orf116; GLUD1; MINPP1 PKD2L1; SCD; WNT8B; SEC31B; NDUFB8; 102069073 102894303 HIF1AN; PAX2; FAM178A; SEMA4G; 10 --- C10orf2; PDZD7; SFXN3; KAZALD1; TLX1 PTPRE; MKI67; MGMT; GLRX3; PPP2R2D; BNIP3; DPYSL4; INPP5A; UTF1; VENTX; 129794743 135346743 Non-commercialADAM8; TUBGCP2; CALY; ECHS1; PAOX; MTG1; CYP2E1 DAGLA; C11orf9; C11orf10; FEN1; FADS1; FADS2; FADS3; RAB3IL1; BEST1; FTH1; INCENP; SCGB1D1; SCGB2A1; SCGB1D2; SCGB2A2; ASRGL1; SCGB1A1; AHNAK; TUT1; MTA2; EML3; ROM1; B3GAT3; GANAB; INTS5; C11orf48; UBXN1; BSCL2; GNG3; HNRNPUL2; POLR2G; TAF6L; TMEM223; NXF1; STX5; WDR74; SLC3A2; SLC22A6; SLC22A8; RARRES3; HRASLS2; PLA2G16; RTN3; C11orf95; MARK2; 11 61481191 68034137 --- NAA40; COX8A; OTUB1; MACROD1; FLRT1; STIP1; DNAJC4; VEGFB; FKBP2; PLCB3; BAD; GPR137; C11orf20; ESRRA; TRMT112; RPS6KA4; SLC22A11; NRXN2; RASGRP2; PYGM; SF1; MAP4K2; MEN1; EHD1; ATG2A; PPP2R5B; ARL2; SNX15; SAC3D1; NAALADL1; ZFPL1; C11orf2; TM7SF2; ZNHIT2; FAU; MRPL49; CAPN1; POLA2; CDC42EP2; DPF2; FRMD8; NEAT1; LTBP3; SSSCA1; FAM89B; EHBP1L1; KCNK7;

5 MAP3K11; SIPA1; RELA; KAT5; OVOL1; MUS81; EFEMP2; CTSW; FIBP; CCDC85B; FOSL1; C11orf68; DRAP1; SART1; BANF1; CST6; SF3B2; PACS1; KLC2; RAB1B; YIF1A; CD248; RIN1; BRMS1; B3GNT1; SLC29A2; MRPL11; DPP3; BBS1; ZDHHC24; ACTN3; CTSF; CCDC87; CCS; RBM14; RBM4; RBM4B; SPTBN2; C11orf80; RCE1; LRFN4; PC; RHOD; KDM2A; ADRBK1; SSH3; POLD4; CLCF1; RAD9A; PPP1CA; RPS6KB2; PTPRCAP; CORO1B; TMEM134; AIP; PITPNM1; CDK2AP2; CABP2; GSTP1; NDUFV1; TBX10; ALDH3B2; ALDH3B1; NDUFS8; TCIRG1; CHKA; SUV420H1; C11orf24 PXN; SIRT4; PLA2G1B; MSI1; TRIAP1; GATC; SRSF9; DYNLL1; RNF10; POP5; CABP1; MLEC; UNC119B; ACADS; HNF1A; C12orf43; OASL; P2RX7; P2RX4; CAMKK2; ANAPC5; RNF34; TMEM120B; RHOF; SETD1B; HPD; PSMD9; BCL7A; MLXIP; 12 120675906 124930486 --- B3GNT4; DIABLO; VPS33A; CLIP1; ZCCHC8; RSRC2; KNTC1; DENR; HIP1R; VPS37B; ABCB9; OGFOD2; ARL6IP4; MPHOSPH9; CDK2AP1; SBNO1; SNRNP35; TMED2; EIF2B1; TCTN2; ATP6V0A2; CCDC92; NCOR2 FLRT2; GALC; GPR65; KCNK10; SPATA7; 14 86045378 90590151 PTPN21; ZC3H14; FOXN3; PRO1768; only --- EFCAB11; TDP1; KCNK13 GPR176; SRP14; BUB1B; PAK6; PLCB2; IVD; BAHD1; RPUSD2; RAD51; FAM82A2; GCHFR; DNAJC17; PPP1R14D; SPINT1; 15 40153012 42534242 CHAC1; CHP; OIP5; NUSAP1; NDUFAF1; use --- RTF1; ITPKA; LTK; RPAP1; TYRO3; MGA; MAPKBP1; SPTBN5; EHD4; VPS39; TMEM87A POLR3K; SNRNP25; RHBDF1; MPG; NPRL3; HBQ1; LUC7L; RGS11; ARHGDIG; PDIA2; AXIN1; MRPL28; TMEM8A; NME4; DECR2; RAB11FIP3; SOLH; PIGQ; RAB40C; RHOT2; RHBDL1; STUB1; METRN; FAM173A; NARFL; MSLN; GNG13; LMF1; SSTR5; CACNA1H; TPSG1; TPSAB1; TPSD1; UBE2I; BAIAP3; C16orf42; UNKL; CLCN7; TELO2; TMEM204; IFT140; HN1L; MAPK8IP3; NME3; MRPS34; SPSB3; NUBP2; IGFALS; 100305 3266053 HAGH; SEPX1; RPL3L; SNORA64; TBL3; GFER; SYNGR3; SLC9A3R2; NTHL1; TSC2; PKD1; RAB26; MLST8; PGP; E4F1; 16 DNASE1L2; ECI1; RNPS1; ABCA3; CCNF; --- C16orf59; NTN3; ATP6V0C; AMDHD2; Non-commercialCEMP1; PDPK1; KCTD5; SRRM2; TCEB2; PRSS21; PRSS22; KREMEN2; PAQR4; PKMYT1; CLDN9; CLDN6; TNFRSF12A; HCFC1R1; THOC6; MMP25; IL32; MGC3771; ZNF205; OR1F1; OR1F2P MAP1LC3B; ZCCHC14; JPH3; KLHDC4; SLC7A5; CA5A; BANP; CYBA; MVD; PIEZO1; CDT1; APRT; GALNS; TRAPPC2L; CBFA2T3; 87432090 90100193 CDH15; ANKRD11; SPG7; RPL13; CPNE7; DPEP1; CHMP1A; CDK10; SPATA2L; C16orf7; ZNF276; FANCA; TCF25; MC1R; TUBB3; DEF8; DBNDD1; C16orf3; GAS8 FOXK2; WDR45L; RAB40B; FN3KRP; FN3K; 17 80520037 80955676 --- ZNF750; TBCD; B3GNTL1 PPAP2C; MIER2; THEG; SHC2; MADCAM1; CDC34; GZMM; BSG; HCN2; FGF22; RNF126; FSTL3; PALM; C19orf21; PTBP1; LPPR3; 19 286240 3739527 AZU1; PRTN3; ELANE; CFD; MED16; --- C19orf22; ARID3A; WDR18; C19orf6; CNN2; ABCA7; HMHA1; POLR2E; GPX4; SBNO2; STK11; ATP5D; CIRBP; C19orf24; EFNA2;

6 MUM1; NDUFS7; GAMT; DAZAP1; APC2; MEX3D; MBD3; UQCR11; TCF3; ATP8B3; SCAMP4; CSNK1G2; BTBD2; MKNK2; IZUMO4; AP3D1; DOT1L; PLEKHJ1; SF3A2; AMH; OAZ1; LSM7; SPPL2B; TIMM13; LMNB2; GADD45B; GNG7; SGTA; THOP1; ZNF556; TLE6; TLE2; AES; GNA11; GNA15; S1PR4; NCLN; NFIC; DOHH; FZR1; C19orf28; HMG20B; TBXA2R; C19orf29; PIP5K1C; TJP3 GDF5; CEP250; ERGIC3; FER1L4; SPAG4; 34023588 34271942 CPNE1; RBM12; NFS1 20 --- RAB22A; VAPB; STX16; NPEPL1; GNAS; 56913665 57888272 TH1L; CTSZ; TUBB1; ATP5E; SLMO2; EDN3 DGCR9; DGCR11; DGCR2; TSSK2; DGCR14; GSC2; SLC25A1; CLTCL1; HIRA; MRPL40; UFD1L; CDC45; CLDN5; SEPT5; TBX1; 19006553 20901902 GNB1L; C22orf29; TXNRD2; COMT; ARVCF; DGCR8; TRMT2A; RANBP1; ZNF74; KLHL22; MED15 APOBEC3G; CBX7; PDGFB; RPL3; SYNGR1; TAB1; MGAT3; SMCR7L; CACNA1I; GRAP2; 22 --- TNRC6B; ADSL; SGSM3; MKL1; MCHR1; SLC25A17; ST13; XPNPEP3; RBX1; EP300; RANGAP1; ZC3H7B; TEF; TOB2; ACO2; 39478378 43572883 CSDC2; PMM1; PPPDE2; NHP2L1; C22orf46; CCDC134; SREBF2; CENPM; NAGA; NDUFA6; TCF20; RRP7A; SERHL2; POLDIP3; CYB5R3; A4GALT; ARFGAP3; only PACSIN2; TTLL1; BIK; MCAT; TSPO; TTLL12

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