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Supplementary Data 2, Zhu Et Al. 2018 A Supplementary Data 2, Zhu et al. 2018 In the motif matching, 20-bp-long primary motifs generated with an automatic pipeline were used, see Methods for details. All discovered motifs are also illustrated in the following pages. Supplementary Data 2 | Motif-based analysis for NCAP-SELEX. a, Due to the fixed adaptors of the SELEX ligand, TFs may also have positional preferences in the HT-SELEX library (Extended Data Fig. 6a). To more clearly visualize the positional preferences induced by nucleosome, the E-MI diagonals from NCAP-SELEX are normalized against those from the corresponding HT-SELEX. Specifically, the E-MI diagonal of each library is first divided by its total strength, then E-MI difference between the NCAP- and HT-SELEX libraries were calculated, and linearly normalized to (0,1) for each TF. TFs are arranged according to the E-MI clustering in Fig. 3a for comparison. The colouring scheme for TF families is indicated. b, Motif matching results for NCAP-SELEX with the 147-bp ligand (lig147). TFs are arranged according to the E-MI clustering in Fig. 3a to facilitate comparison. The motif matching result is oriented radially and scaled for each TF. c, Motif hits ratio (log scale) between the bound and the unbound cycle 5 libraries. The hits of each library were normalized by number of total reads of the library. TFs are arranged according to the clustering in Fig. 5a for comparison. d, Motif matching results of NCAP-SELEX with the 200-bp ligand (lig200). TFs are arranged according to the E-MI clustering in Extended Data Fig. 2a for comparison. (bp) a 1 Znf_GATA Znf_C2H2 96 T_box RUNT RHD RFX POU PAX Nuclear_receptor MYB MEIS MADS IRF HSF Homeodomain HMG Forkhead ETS E2F CUT CSD bZIP bHLH AP2 Normalized E-MI b Znf_GATA Motif hits Znf_C2H2 T_box RUNT RHD RFX POU PAX Nuclear_receptor MYB MEIS MADS IRF HSF Homeodomain HMG Forkhead ETS c E2F CUT CSD bZIP bHLH AP2 1.67 0 -0.62 Log2(Hitsunbound/Hitsbound) d Znf_GATA Znf_C2H2 T_box RUNT RHD RFX POU PAX Nuclear_receptor MYB MEIS MADS IRF HSF Homeodomain HMG Forkhead ETS E2F CUT CSD bZIP bHLH AP2 Motif hits Automatic primary motif discovery (NCAP-SELEX, lig147) VSX1 MEIS2 FOXE1 NFATC3 NKX2−4 2 0 TBX3 FOXA2 CREB3L4 MAFA RAX 2 0 HOXD10 MNX1 CUX1 NFATC1 ETV5 2 0 TFAP2B NFKB2 TFAP2C NFATC2 NFATC4 2 0 ZIC1 ATF2 RFX4 POU3F2 CREB5 2 0 RFX2 SREBF1 PAX1 TFAP4 NR3C2 2 0 Bits OTX2 LBX2 TGIF2LY GATA4 CREB3L1 2 0 HOXB7 GATA6 ATF3 TBX21 TFEB 2 0 BHLHB8 TCF12 MYBL1 ETV4 EOMES 2 0 SOX18 JUND POU4F2 DLX2 POU1F1 2 0 PITX1 POU3F4 GSX2 POU2F3 GSX1 2 0 POU4F3 DUXA VENTX MLX ELF1 2 0 Automatic primary motif discovery (NCAP-SELEX, lig147) ELF4 USF2 MIXL1 HSF1 FOXI1 2 0 TGIF2LX HSF4 BHLHA15 ONECUT2 ATOH1 2 0 TBX4 DRGX ERG ETV1 FLI1 2 0 OLIG2 TBX2 EVX2 CREM E2F8 2 0 THRB PAX7 PAX2 CDX1 SOHLH2 2 0 DLX5 SREBF2 DLX4 DLX1 CREB1 2 0 POU2F2 HOXC11 HMBOX1 ELF5 ESX1 Bits 2 0 NR4A2 RUNX3 PROX1 VSX2 GLI3 2 0 BHLHE22 MYBL2 LMX1A ELK3 IRX5 2 0 NKX2−3 MYOG SOX10 RFX1 TLX2 2 0 FOXB1 IRX1 FOXJ2 MAF CEBPE 2 0 GATA3 MSX1 ELF2 IRF8 CLOCK 2 0 Automatic primary motif discovery (NCAP-SELEX, lig147) LMX1B RFX3 FEV BHLHB2 MEIS3 2 0 TFEC YBX1 SPIB T HOXC10 2 0 TFE3 TCF4 MAFG MSX2 CEBPB 2 0 NHLH1 LEF1 JUND2 FOXD3 ARX 2 0 GATA2 FOXD2 XBP1 HOXA10 PITX2 2 0 DMBX1 IRF3 PROP1 VAX2 BARHL1 2 0 SHOX PKNOX2 SOX7 ZGLP1 RFX5 Bits 2 0 HES2 ALX3 SOX14 FIGLA EN2 2 0 SOX11 SOX12 HOXA2 FOXO6 POU4F1 2 0 FOXK2 TGIF2 FOXO1 HOXD12 HES5 2 0 HOXD3 SIX6 NKX6−2 HMX1 GSC2 2 0 NANOG SRF OTX1 ARGFX FOXK1 2 0 Automatic primary motif discovery (NCAP-SELEX, lig147) MLLT7 PITX3 ZNF690 ZIC4 HOXB13 2 0 SOX2 VAX1 MYCN PHOX2B HOXD4 2 0 PDX1 EVX1 EN1 ISL1 PRRX1 Bits 2 0 HOXD9 2 0 Automatic primary motif discovery (NCAP-SELEX, lig200) VSX1 NFATC3 TBX3 CREB3L4 MAFA 2 0 RAX HOXD10 CUX1 NFATC1 ETV5 2 0 TFAP2B TFAP2C NFATC2 NFATC4 ZIC1 2 0 ATF2 RFX4 POU3F2 CREB5 VAX2 2 0 FOXA2 RFX2 SREBF1 PAX1 NR3C2 2 0 LBX2 TGIF2LY GATA4 CREB3L1 HOXB7 2 0 SD1 Bits EOMES ATF3 TBX21 TFEB BHLHB8 2 0 ETV4 DLX2 POU1F1 PITX1 SOX11 2 0 GSX2 PAX5 POU4F3 DUXA VENTX 2 0 MLX ELF1 ELF4 PKNOX1 USF2 2 0 RFX1 MIXL1 HSF1 FOXI1 TGIF2LX 2 0 HSF4 BHLHA15 ONECUT2 ATOH1 TBX4 2 0 Automatic primary motif discovery (NCAP-SELEX, lig200) DRGX ERG ETV1 FLI1 UBP1 2 0 TFCP2L1 TFEC TFCP2 OLIG2 EVX2 2 0 SOX12 THRB PAX7 PAX2 CDX1 2 0 SOHLH2 DLX5 SREBF2 DLX4 OTX1 2 0 DLX1 SRF CREB1 POU2F2 HMBOX1 2 0 ELF5 ESX1 GLI3 NR4A2 PROX1 2 0 Bits RFX3 VSX2 BHLHE22 MYBL2 IRF7 2 0 SOX10 ELK3 NKX2−3 FOXB1 MAF 2 0 CEBPE MSX1 ELF2 CLOCK LMX1B 2 0 FEV BHLHB2 MEIS3 YBX1 SOX9 2 0 HOXC10 TFE3 MAFG MSX2 HOXD4 2 0 ATF4 IRF8 CEBPB PDX1 NHLH1 2 0 Automatic primary motif discovery (NCAP-SELEX, lig200) EVX1 JUND2 FOXD3 ARX GATA2 2 0 FOXD2 XBP1 HOXA10 PITX2 DMBX1 2 0 IRF3 EN1 PROP1 BARHL1 SHOX 2 0 PKNOX2 SOX7 RFX5 MNX1 ALX3 2 0 FIGLA E2F4 EN2 SOX3 FOSB 2 0 SOX4 SOX8 BSX ISX SOX18 2 0 Bits JUND GSX1 PROX2 POU4F2 HOXD12 2 0 HOXD3 NEUROG1 HOXA9 CREM E2F8 2 0 GSC2 NANOG HOXD13 TBX2 HSF2 2 0 ARGFX LMX1A TCF15 HOXB5 RHOXF1 2 0 RUNX3 MLLT7 PITX3 HOXB13 MYOG 2 0 TLX2 FOXJ2 HELT T ZNF597 2 0 Automatic primary motif discovery (NCAP-SELEX, lig200) ZIC3 SNAI2 SNAI1 OVOL2 YY1 2 0 ZNF32 ZNF524 OVOL1 KLF13 ZNF821 2 Bits 0 KLF12 CTCF 2 0.
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