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Supplementary Fig. 1

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Smarce1 Pttg1ip

Foxa2 Ciao1 Akt1 Stat5b

Hcfc1 Fosl2 Lck Pus1

Pax5 Mycn

Klf13 Tfam

Chd4

Mapk11

Hist1h3d Hck Gpc1

Mapk14 Smad2

Etv1 Mxd3

Cdk7 Thap11

Ctcf Eno1

Zfp219 Bcl3 Cbx5

Hsf1 Ripk2

Ngf Rela Bcl10

Ddx5 Eef1a2

Trp53

Dummy

Rnf14 E2f4 Zfp367

Cdc5l Wdr77

Brca1 Scand1 Usf1

Zeb1

Abt1 Cand1 Ran Thrap3

Spi1

Pias1Il6raIl21

Runx1 E2f1 NfiaEsr1

Sp3

Taf6l Sin3b

Gtf3a G

tf2a1 Sp1

Tfap2c Nfic

Med27 Med30 Tnf Hdac3

Hdac2 Med21 Ctnnb1 Mmp7 Jun

Sra1 Fos

Btk Nfy

Ebf1 Litaf

Pou5f1 Ncor1

Rara Adrbk1 Prkcg Ctcfl

Rxra

Prpf6 Dmtf1Gtf2a2

Taf1 Cct4

Kcnip3 Taf10

Polr2a Zkscan17

Stat3 Atf4

Rbl1

Ciita Nfkb1 Ybx1

Nfkbia Mapkapk3 Rps6ka5 F2

Meis2Otx1

Pou3f2 Nr2e1Lhx2 Ctbp2Pou3f3 Gsx2 Tsc22d1

Yeats4

Nrf1

Atf2 NfyaTcerg1

Ssrp1 Sp2Smarcd1 Cir1

Notch3 Jag2 Notch4 Tbpl1

Ncor2

bHmg20b Snd1

Zbtb20 Adam10

Zmiz1 Jup

A2m Nfyc

Baz1b Id1

Il23r Cblb

Rnf2 Il1aMapk1 3 Ccne1

Traf2 Atf1

Tcf7l2 Snai2 Kat2a

Ash2lEtv5 Nfe2l2

Ezh2 Foxa1

Pbx1

Dtx1

Rap1gap2 Rbl2

Atm Tdp2

Tfdp2

Ywhab Prkg1

Trim28 Foxo4 Prkg2

Mapk12 Suv39h1 Tcf3

Mapk8

Gtf2i Ubp1

Cebpa Preb

Tsc22d3

Tcf4 A r Rel

Patz1Ccnd1 Gtf2f1

Pou2f1 Med1 Pparg Cd40lg

Jund Tcf12 Tal1 Usp21 E2f6

Rbbp4 Zfp579 Arid1a

Whsc1

Mettl3Smarca4 Zfp644

Csrp1 Nfkbib

Psmb11 Nr3c1 Rnf4

GmnnZfp422

Med4 Med7

Hnf4a Cops5

Wnt1

sp1 Rbbp7 Ep300

Med23 Med6

Sfrp1

Wnt10b Hdac1 Fzd1 Wnt9b

Ppargc1 Tfdp1

Smarca2 Smarcc1 Myb Fiz1 Yy1

Smarcc Ddx1 Polr3a2

Trrap Psmc5

Myc

Trip6 Dnajc2

Dpf2

Thbs1 Cblc Hif1a

Actl6a Itga1 Egfr

Nfix Psmd9 Plcg2 Hdac4Camk4

Creb1

Hdac5

Ing4 Nr1h2 Hmgb2

Srf

Sub1 Tada3 Ss18 edPsip1 Cdkn2a E

Sox8 Hes6 AsphCarh Tfap2a a Apex1

Ascl1 Batf

Pias2 Ruvbl1 Gabpb1 Npm1 Pbrm1

Btg1 Zeb2

Smad1 Smad3Tgfb1 Srebf1 E2f5 Srebf2Cebpb

Tgif2

Camta1 Hbp1

Adipor1 Ppara Nfx1

Sox9 Gm1862 Neurog3 Rbbp5

Hes1

Prkx Ubtf Ercc6

Max

Notch1

Hes5

Sox2 Adcy4

Yap1 Gnas Axin1

Rbpjl

Srsf2 Pax6

Cen Esr2

Id4 Egr1

Ddx54

Smad9 Ppp2ca Sfn LOC102634437 Csnk1e

Nup98Cenpa Rorb

phGm55 93 C enpk

Npas2 Mapk1

Ngfr Ncstn Irf3

CenpnCenpq AI607873

Sox8

Tada3

Ncor1

Smarca2 MybTsc22d3

Psip1 Mettl3

Cbx5 Zfp579

Zfp644 Zfp422

Nr3c1 E2f6 Cdk7 Hist1h3d

Taf10 Gtf2a2G tf2h3 Tbp

Btg1 Mapk11

Hdac3

Rbpj Fiz1

Notch2

Cops5

Trim28 Ss18

Ascl1 Batf Rorb

Litaf

Bcl3 Eno1 Ddx5 Ing4

Ran Med30

Taf6l

Rnf2 Etv1 Tnf Med27

Usf1 Mapkapk2 Med21

Eed phCarhsp1

Ep300 Yy1 As

Nr1h2 Tcf3

Ubtf Ercc6 Srf

Cdkn2a

Hes6 Tfdp1

Tfap2a Apex1

Smarcc1 Ybx1

F2

Ctbp2 Hbp1

Tcerg1

Nfya Gsx2

Isg15

Aurkb Psmb9 Runx1 Nup43

Irf4

Npm1 Hdac1

Gata3 Stat1

Baz1b Camta1

Nfyb Snd1 Zbtb20 Hmg20b

Ciita

Sp3

Gtf2a1 Sin3b

Gtf3a

aNfia Ddx54 Esr1

Sp1

Jund Arid1a Polr2 Scand1 Tfap2c

Nfic

Cenpa

Trip6 Psmd9

Ddx1 Irf3

da2b AI607873 Ta Eef1a2

Dnajc2 Hdac2 Trp53

Nfe2l2Ezh2

Etv5 Id1 Ash2lFoxa1Pbx1 Polr3a

Actl6a

TrrapPbrm1 Smarcc2

Myc

Ruvbl1 Psmc5 Tdp2 Rbbp5 Nfix

Max Mapk13 Jun Sra1

Ssrp1

Cd40lg Med1

Sp2 Tgfb1

Zeb1 Fos Abt1

Tbpl1 Smarcd1 Spi1

Kat2a Cenph

Cenpq Snai2

Gm5593 Rps6ka5

Hsf1 Nfx1 Atf1 Arrb2

Smarce1

Rbbp7 Pax5

Il2ra Pttg1ip

Stat5a

Mycn Klf13

Pus1

Helz2 Wnt9b

nt10b M ed23 Med4 Med7W

Srebf1 Pparg Pou2f1

Gpc3

Med6

eurog3 Hes1 Pax6N

Hes5 Nfyc

Lrp1

Dummy

Rbpjl Hdac4C

Tbc1d4

alml3 amk4C

Ywhab Ciao1

Bcl10Ripk2 Foxa2

Maged1 Itga1

Lrpap1 Akt1

H2-K1 Plcg2Ntrk2

Reln Dpf2

Ngf Gmnn

Psma8

Nfkbib Snca Hif1a

Pik3cd

Prkx Hck

Sox9 Adcy1 Egfr

Blk Hdac5

S1pr1 Adrbk1

Stat4 Prkcg

Rela Plcb2

Mapk14

Cdk1 E2f1

Cenpn

Cenpk Gabpb1

Zkscan17

Dmtf1

Sdc2 Mnat1

Prkg2 Cct4

Tsc22d1 Taf1 Pias2

Gtf2i

Srsf2 Lhx2

Ccne1

E2f2 Creb1 Prkg1

Rbbp4 Gm5601

Mapk8 Tcf4

Gtf2f1 Preb

Ubp1

Cebpa

A r Ncor2

Rnf4

Cdc5l Atf4 Brca1

Cand1 Wdr77 Rad21

Cdk6

Suv39h1 Csrp1 Patz1 Rel

Chd4

Sox2 Pou5f1

Atf3 Hmgb2

Cebpb Tal1

Sub1 Whsc1

Usp21 Tcf12

Pou3f2 Nr2e1 Pou3f3 Otx1

Meis2 Zfp367

Mapk3

Rbl1 Cdkn1a Rbl2Tfdp2 Ctcf

E2f5 E2f4

Mxd3

Smad4

Pias1 Zmiz1

Tcf7l2

Il6 Hnf4a

Hcfc1 Nfkbia

Smad1 Atf2

Bmpr1b Bmp2 Id4

Smad2

Smad9S

Zeb2

mad6Smad3Tgif2

Yeats4

Srebf2 Rxra Cir1 Notch3

Nrf1

Zfp219 Smarca4 Dtx1

Ctcfl

Tfam Snapc2

Ets1 Kcnip3

Egr1 Thrap3

Mmp7 Ctnnb1

Prpf6

Supplementary Fig. 1

Inferred Steiner trees for quiescent and active NSCs. It can be seen that the dummy node in the center is the root node that connectes with all receptors/ligands. The inverted triangles depict receptor molecules, circles

depict signaling intermediates and squares depict transcription factors.

Quescient NSCs

Active NSCs

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