A Pro-B LTr pre-B Upregulated Upregulated 3 3

2 2

1 1

0 Mean count 0 Mean count <15 15-50 50-500 500-1000 1000< <15 15-50 50-500 500-1000 1000< Fold Change Fold Change 2 -1 2 -1 Log Log -2 -2

-3 -3 Downregulated Downregulated B Term Change –Log10(P) Description GO:0098609 Up 10.421047 Acvr1,Adrb2,Alcam,Bmp4,Cd6,Cd86,Cdh15,Cxadr,Dsg2,Efnb1,Efnb2,Ephb4,Erf,Gstp1,Icam1,Itgam,Itgb5,Aju cell-cell adhesion ba,Jup,Kifc3,Krt18,Lag3,Lama3,Prkcq,Prkcz,Ptprf,Nectin2,Rag1,Rara,Ccl25,Sell,Spint2,Tgfb2,Tyro3,Vcl,Xbp1 ,Zap70,Zbtb7b,Podxl,C1qtnf1,Nectin3,Clstn1,Kirrel3,Tnfaip8l2,Megf10,Dusp3,Izumo1,Vsir,Mcam,Pcdhgc3,Pc dhga4,Pcdhga12,Pag1,Amigo2,Il1rl2,Pawr,Fgfrl1,Plxnb3,Smagp,Megf11,Cd300a,Clstn3,Plekha7,Cadm4,Jaml ,Adgrl1,Scarf1,Itgad GO: 0030334 Up 13.408973 Ada,Adam15,Angpt1,Rhob,Rhod,Arhgap5,Eng,Ptk2,Fgfr1,Gab1,Gab2,Gna12,Cmklr1,Igf1r,Itga5,Kdr,Kit,Abcc regulation of cell migration 1,Myo1f,Pgf,Pld2,Sema4a,Sema4c,Sema7a,Tgfbr3,Tiam1,Tie1,Trip6,Vegfa,Ldlrad4,Plxnc1,Plxnd1,Dab2ip,Sa sh1,Robo4,Amotl1,Mctp1,Abr,Tbc1d24,Igsf10,Smo,Egfl7,Glipr2 GO:0045926 Up 6.4073906 Aatk,Adam15,Adrb2,Bmp4,Cd36,Cxadr,Ptk2,Fbp1,Fhl1,Gng4,H19,Lta,Enpp1,Ptprs,Sema4a,Sema4c,Sema7a * negative regulation of growth ,Tgfb2,Sema4g,Tro,Rrad,Dcbld2,Gas2l1,Nkd1,Socs2,Sesn2 GO:0010942 Up 4.1342234 Adrb2,Agrn,Axin2,Bmp4,Camk2a,Cd36,Col18a1,Efnb2,G0s2,Lpar1,Grik5,Itgam,Lrp1,Lta,Ltbr,Mef2c,Neurl1a, ** positive regulation of cell death Ptprf,Rps6ka2,Ccl3,Sort1,Tsc22d1,Tgfb2,Timp3,Trp63,Unc13b,Xbp1,Zfp13,Phlda3,Foxo1,Cd248,Clip3,Trps1, Pawr,Adamtsl4,Map3k9 GO:1903047 Down 20.674194 Bub1,Ccna2,Cdc7,Foxm1,Id2,Kif11,Aurkb,Top2a,Racgap1,E2f7,Pidd1,Spc25,Nuf2,Fbxo5,Kif18b,Kif23,Kif2c, mitotic cell cycle process Cep55,Tcf19,Cenpf,Nusap1,Kif22,Rad51c,Rtkn2,Gen1,Kif18a,Clspn,Ccnf,Epb41l2,Nek3,Spc24,E2f8,Esco2,K if15,Dnah8,Map1a,Pclaf,Snap29,Stx11,E030030I06Rik,Trappc5,Daglb,2810006K23Rik,Lrr1,Kbtbd6 R-MMU-156590 Down 4.7559489 Esd,Gclm,Gss,Mgst1,Mtrr,Cyp39a1,Prkag2,Acot2,Kyat3 Glutathione conjugation GO:0030098 Down 6.9511677 Blk,Socs1,Dtx1,H2Aa,Il2ra,Ly6d,Pou2f2,Rasgrp1,Syk,Polm,Dusp10,Card11,Itgb3,Nfkbia,Gpr171,Zc3h12d,Sw lymphocye differentiation ap70,Egfl6,Carmil1,Cd2,H2Eb1,Il5ra,Nrxn1,Fcgr2b,Il33,Tirap,Gcsam,Hck,Sdc1,Prkcg,Sema4b,Hspa2 Cd2 Cd2 Blue: commonly up or down regulated between ΔChd4 LTr pre-B and ΔIkE5 large pre-B Red: commonly up or down regulated between ΔChd4Cd2 and ΔEbf1Cd19 large pre-B Green: commonly up or down regulated between ΔChd4Cd2 LTr pre-B, ΔIkE5Cd2 large pre-B and ΔEbf1Cd19 large pre-B Bold: Shown on genome browsers in Figure 6 and Supplemetal Fig.6. * This pathway was enriched in “807 (124+683)” genes in the venn diagram in Figure 4C. ** This pathway was enriched in “683” genes in the venn diagram in Figure 4C. C ) ) Esd Gclm ) Gss ) Mgst1 2 2 2 2 9 8 4 5 8 7 7 6 3 4 6 5 3 5 4 2 4 2 3 3 2 2 1 1 1 1 0 0 0 0 Read counts (x10 Read counts (x10 Read counts (x10 Read counts (x10 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 Δ Cd2 Δ Cd2 Δ Cd2 Δ Cd2 WT Chd4 PreB_1 LTr PreB_2 LTr PreB_1 LTr PreB_2 LTr WT Chd4 PreB_1 LTr PreB_2 LTr PreB_1 LTr PreB_2 LTr WT Chd4 PreB_1 LTr PreB_2 LTr PreB_1 LTr PreB_2 LTr WT Chd4 PreB_1 LTr PreB_2 LTr PreB_1 LTr PreB_2 LTr WT ΔChd4Cd2 WT ΔChd4Cd2 WT ΔChd4Cd2 WT ΔChd4Cd2 ) ) ) ) 2 Mtrr Cyp39a1 2 Prkag2 2 Acot2 2 7 7 10 3 6 6 8 5 5 2 4 4 6 3 3 4 2 2 1 1 1 2 0 0 0 Read counts (x10 Read counts (x10 0 Read counts (x10 Read counts (x10 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 ProB_1 ProB_2 Δ Cd2 Δ Cd2 Δ Cd2 Δ Cd2 WT Chd4 PreB_1 LTr PreB_2 LTr PreB_1 LTr PreB_2 LTr WT Chd4 PreB_1 LTr PreB_2 LTr PreB_1 LTr PreB_2 LTr WT Chd4 PreB_1 LTr PreB_2 LTr PreB_1 LTr PreB_2 LTr WT Chd4 PreB_1 LTr PreB_2 LTr PreB_1 LTr PreB_2 LTr WT ΔChd4Cd2 WT ΔChd4Cd2 WT ΔChd4Cd2 WT ΔChd4Cd2 Yoshida_Fig.S4