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Suppl Fig 3 Revised2 Cornelissen_FigS3 A sgScr #1 sgTrps1 #1 B C sgScr sgTrps1 sgScr #1 sgTrps1 #1 sgScr #1 sgTrps1 #1 Il15 #1 #2 #1 #3 Irf4 Full medium + + + + - - - - Socs1 Cdkn1a Ccl2 STAT1 DIP mix - - - - + + + + Cd74 Il4ra Selp shNT - - + - + - + - Cd38 Tapbp shSTAT1 Ogfr TRPS1 - + - + - + - + Ptpn1 Sri Psmb2 phospho-STAT5 Oasl1 Uba7 β-actin Ciita Txnip Mthfd2 Myd88 Casp8 β-actin Il7 Cxcl10 STAT2 Zbp1 Ripk2 Psmb9 Itgb7 total-STAT5 Gch1 TRPS1 Ccrl2 Lgals3bp Il6 Psmb8 Parp14 β-actin Ifi35 β-actin Ripk1 Stat3 Arid5b Socs3 Irf7 Trim25 Stat1 D E F Peli1 Stat1 Apol6 Full medium β-casein Pml + + - - Irf9 DIP mix - - + + 1.5 n 1.5 o Trafd1 n i o ) Trim21 s ** BSA *** ) + - + - i 0 s Eif2ak2 0 s 2 e Sspn 2 IFNγ - + - + s r S Parp9 S e p r Bst2 P P x Elf1 p R phospho-STAT5 R 1.0 e 1.0 x Trim14 o o e Isg15 n t t i Ube2l6 1 e d t Xaf1 d s e e Ifi44 β-actin a t a z z i Samd9l i c l l S - Ddx60 a a e Stat2 0.5 β 0.5 m v Ddx58 m e i r r t Ifit2 v o o i total-STAT5 a Jak2 l t n n ( Hif1a ( e a Slc25a28 l R Nod1 e Pim1 β-actin R Bpgm 0.0 0.0 Adar IFNγ Tap1 - - + - - + IFNγ Pfkp Sppl2a - + + DIP mix - + + DIP mix Cmpk2 Rsad2 Oas2 G Vamp8 H Ifih1 Myogenesis Nampt Tdrd7 Psma3 sgScr #1sgTrps1 #1 sgScr #1sgTrps1 #1 Interferon Gamma Response Rtp4 Nub1 BSA KRAS Signaling down Oas3 + + - - B2m IFNγ TNFα signaling via NFκB Casp3 - - + + Pnpt1 Inflammatory Response Il10ra phospho-STAT1 Stat4 Lysmd2 P53 Pathway Dhx58 St3gal5 Interferon Alpha Response Upp1 β-actin Vamp5 UV Response up Lcp2 Ptpn2 March1 Epithelial Mesenchymal Transition Tnfsf10 total-STAT1 Nmi Estrogen Response Late Ifi44l 1700057- Cd86G04Rik Vcam1 β-actin 0 1 2 3 4 5 St8sia4 Bank1 -log10(FDR) Cd40 Cxcl9 Psme1 Ncoa7 Gmpr Lpar6 I DMSO Rnf213 + - Il2rb TSA P2ry14 - + Znfx1 Procr Il18bp STAT1 Batf2 Cmklr1 Icam1 Arl4a Mov10 β-actin Irf2 Herc6 Trim26 Csf1 Auts2 Mettl7b STAT2 Parp12 Ncoa3 Pde4b Pla2g4a Eif4e3 β-actin Tnfaip3 Wars Irf5 H2-DMa Nlrc5 Casp7 Cnp Cd274 Cd47 Irf1 Nfkbia Nfkb1 Il15ra Tmem140 Ptgs2 Tnfaip6 1.5 Tor1b Rbck1 Cxcl11 1.0 Mvp Nup93 0.5 Btg1 Tnfaip2 0.0 Ly6e Isg20 Lap3 (Z-score) -0.5 Expression Samhd1 Ptpn6 -1.0 Fas Isoc1 Psmb10 Supplementary Figure S3. Reduced TRPS1 expression increases interferon signaling thereby affecting normal function of HC11 cells. (A) Heatmap reflecting gene expression at the genes listed in the interferon alpha and interferon gamma gene lists from the Hallmark Gene Sets collection shown in Figure 3D, with all genes annotated. (B) Western blot analysis of STAT1 and STAT2 expression levels in HC11 control and TRPS1 knockout clones. β-actin was used as a loading control. (C) Western blot analysis of phosphorylated and total STAT5 levels in HC11 control and TRPS1 knockout cells transduced with a non- targeting shRNA or a pool of shRNAs targeting Stat1 in full medium or upon treatment with DIP mix. β- actin was used as a loading control. (D) Western blot analysis of phosphorylated and total STAT5 levels in IFNγ (30ng/ml) treated HC11 cells in full medium or upon treatment with DIP mix. β-actin was used as a loading control. (E,F) RT-qPCR analysis of Stat1 (E) and β-casein (Csn2) (F) expression levels upon treatment with DIP mix and/or IFNγ (30ng/ml). Data represent mean+SD, n=2. T-test: *** p<0.001, ** p<0.01. (G) Western blot analysis of phosphorylated and total STAT1 expression levels in HC11 control and TRPS1 knockout cells upon treatment with IFNγ (30ng/ml). β-actin was used as a loading control. (H) Pathway enrichment analysis performed on RNA-seq of HC11 cells treated with or without TSA (300nM), using the MSigDB Hallmark GeneSet Collection (Liberzon et al. 2015). FDR<0.05 was considered significant. The interferon signaling pathways are highlighted in green. (I) Western blot analysis of STAT1 and STAT2 expression levels in HC11 cells treated with or without TSA (300nM). β-actin was used as a loading control. 5 .
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