Supplemental Table 1:Genes That Define the Differentiation from P1 to P4 in the Colon

Supplemental Table 1:Genes that define the differentiation from P1 to P4 in the colon

t-test: P1 vs P4; PRaw≤ 0.05; Fold Change ≥ 2.0

Downregulated from P1 to P4 / Upregulated from P1 to P4
Gene Symbol / Fold Change / Gene Symbol / Fold Change
Ripk2; Kpna2; Syne3; A630033H20Rik; Traf1; Ifitm3; Megf9; Unc119b; Styx; Pgk1; Lrrc8b; Arg1; Sept9; Mdm1; Gramd4; Flot2; Prkag2; Pgd; Oasl2; Ramp1; Cish; Gm10268; Piezo1; Nod2; Nbeal2; Rcl1; Slfn8; Tkt; Ccl9; Agpat4; Emb; 1110007C09Rik; Pgam1; Nab1; Id3; Myd88; Naaa; Pqlc3; Mki67ip; Ppp2cb; Chd7; Ccl24; Fkbp5; Gm4876; Sp110; Sp110; Herc4; Stx3; Dmkn; Pgk1; Pgk1; Fbxo28; Rarg; Sept6; Rnh1; Eno1; Setdb2; Abcd2; Isg20l2; Zkscan6; Rsl24d1; Zcchc2; Foxn2; Sorl1; Cyp4f16; Cd300lg; Ptpn1; Mocos; Chi3l4; Avpi1; Tmsb10; Nr4a2; 2610018G03Rik; Crybb1; Mocs1; Chn2; Gnb2l1; Cast; Trmt112; Sod2; Slc24a6; Scarb1; Dgat2; Sms; Spink2; Gch1; Pstpip1; Abca7; Dock5; Cbfa2t3; E2f2; Abcc4; Alpk1; Bcl3; Vps13c; Rab27a; Tmsb10; Oas2; Aldh2; Fosl1; Eno1; C1galt1c1; Csprs; Myadm; Clec4d; Csf3r; Ndnf; Haao; Esyt1; Tstd3; Ldlr; Dram1; Impa2; Dusp3; Anxa1; Sms; Mfsd7a; Elmo2; Itga1; Scnn1a; Osm; Eps8; Tiam2; Ikbkb; Ppp1r15b; Cyp2ab1; Pira1; Ms4a4b; Pkm; Map3k15; Plcg2; Gm14005; Tmem156; Rgs18; Hmha1; H60b; Lmo1; Ccdc125; Ppp2r5a; Rasgrp4; Nadk; 2410091C18Rik; Lsr; Csf3; Pot1b; Tmem71; G6pdx; Lcn2; Gm1966; Slk; Fbxo4; Mob3b; Pira11; Tmpo; Uck2; Sgms1; Isg20; Zbp1; Tmc8; n-R5s180; Gm1673; Ankrd28; Lbr; Rara; Atp2a3; Ccdc71l; Ppp2r5a; Chd7; Snai1; A530023O14Rik; Kcnab2; Tmc6; Samd9l; Gapt; Map4k1; Slfn5; Ampd3; Itgal; Trp53bp2; Lmbr1l; Padi2; Ccl6; LOC100505155; Slc22a15; Itpr1; Mrpl33; S100a6; Prkce; Samsn1; Cyp39a1; Agtpbp1; Spata13; Mbnl3; Gadd45a; Fabp7; Me2; Diap2; Padi4; Plec; Gyk; Mx1; Atp10a; Ppp2r5a; Coro2a; Adssl1; Ppp2r5a; Ankrd37; Sestd1; S100a10; Sp100; Nupr1; Ptgir; Bcl11a; Nfam1; Vcl; Rhou; Diap1; Gm4955; Il17ra; Stxbp6; Ccr2; Prkx; Helz2; Gpr35; Jarid2; Ear10; Alcam; Samhd1; Adora2a; Fgr; Ctse; Ctse; Irgm1; Fbxl5; Bin2; Klhl2; Irg1; B430306N03Rik; Atp1a3; Bst1; Taf1d; Rgcc; Ear1; Mfsd6; Smpdl3b; Irak3; Zyx; Nedd9; Gpcpd1; Ahnak; Cers6; Ear10; Fmnl1 / ≥2.0 / Dnajb4; Fam189a2; Mafb; Gm7120; Sesn3; Clmp; Tmem206; Siglece; Fgd2; Eprs; Ifitm1; Bpnt1; Mef2c; Mid1; Pald1; Fam214a; Tsku; Dut; Plekhn1; Usp37; Fam212a; Rapgef2; Kbtbd3; Gaa; Mir212; Irf8; Rnase4; Rasgef1b; Arhgap19; Nfatc2; Rbpj; Uaca; Bag3; Abca9; Hbb-b2; Nceh1; Fnbp1; Rgs10; Flnb; Hk2; Tnni3; Rcn3; Rhoc; Slc46a1; 1110058L19Rik; Ada; Capns2; Swap70; B230118H07Rik; Trdn; Klhl18; Kmo; A730008H23Rik; Prim2; Zfp667; 1500011K16Rik; Tnf; Inpp5e; Rab11fip5; C1qtnf1; Man1a; Cystm1; Camk1; Hes1; Tdp1; Tspyl2; Cxcl13; Slc7a4; Pde3b; Nxt2; Ccdc163; Ttc3; Rnf219; Itpripl2; Pigz; Jmy; Ctsf; Gpr155; 8430410A17Rik; Insl6; Srxn1; Uap1l1; Stard13; Ralgps2; Mcm3; Rasl2-9; Dmxl1; Tubgcp5; Spire1; Syngap1; Xylt2; Myo9a; Ralgds; Wnk1; Cdk5rap2; Eef2k; Stard8; Actg2; Camk2n1; Cdk1; Nrp2; Lgmn; Hic1; Tbcc; Snx29; Cd274; Cx3cr1; C1ra; Mir99a; Slc9a3r2; Slc37a2; Fggy; Tspan32; Fam178a; Gkap1; Il23a; Ngfrap1; Mtmr10; Gpr55; Zfp938; Stat4; Dpp7; Fam178a; Dppa3; St8sia4; Pvt1; Gas2l3; Abcg2; Emr1; Rapsn; Hsd17b4; Src; Bbs9; Tssc4; 5430435G22Rik; Selm; Cd209f; Lpcat1; Slc11a2; Mir1956; Pld3; Wsb2; Cd200r4; Plcb2; Ccdc34; Tbc1d10a; St5; Vipr1; Fam213b; Eif2b2; Plac9; Kif13b; Ttc39b; Plac9; Plac9; Zfp780b; Aga; Sh3pxd2b; Prim1; Sema4b; Tpp1; Cxx1c; Renbp; Adap2; Akr1b10; Pmvk; Psd3; Acss1; Galc; 4930503L19Rik; Pcmtd1; Agpat3; Mt1; Basp1; Dusp19; Tlr3; 9930022D16Rik; Iigp1; Cd79b; Fosb; Cspp1; Slc14a1; vipr1; Gm10522; Cd33; Tgfbr2; Abcb1b; Cebpa; Etv1; Tbc1d19; Wdfy3; 1700009P17Rik; Aif1; Zfp810; Ggt5; Copz2; Soga1; Dyrk2; Tmem140; Man1c1; Prss30; Col14a1; Ctnnd1; Hs3st3a1; Serpinb6a; Cd276; Ulk2; Lancl1; Ermap; Lacc1; Rarres2; Dtx3; Mmp25; Sepp1; Epb4.1l3; Mfhas1; Zcchc14; Lix1l; Tceal1; Pisd-ps1; Pdia4; Ap1b1; Cd74; Sh2d1b1; Mroh2a; Ipo13; Mpa2l; Rhobtb1; Grasp; Acp2; Cxcl10; Mylip; Rcan1; 1110032A03Rik; 0610009B22Rik; Fam46c; Nenf; Akr1e1; Cwc25; Ifitm1; Vkorc1; Fads3; Mki67; Lmna; Gm5129; Inpp4b; Mt2; Ocrl; Fam3c; Serbp1; Tmem86a; Akip1; St3gal6; Tcf21; Nicn1; Ifi27l1; Rmi1; AI427809; Fpr1; Cd36; Dcstamp; Prelid2; St6gal1; Bcl9; Tulp4; Sfmbt1; Zfhx3; Appl2; Slc9a9; Tnfrsf11a; Il21r; Cpne2; Mras; 1110001A16Rik; D17H6S56E-5; Cttnbp2nl; Arhgap10; Apoe; Clec4b1; Adam22; Trim47; Decr2; Tnfsf13b; Adora3; Stmn1; Tfpi; Gm10307; Ctsl; Maged1; Il1rl2; Smc2; Fggy; Tppp; Map4k3; Tspan4; Slc40a1; Rmi1; Lpcat2; Htra1; Arhgap18; Nfxl1; Smad7; Pecam1; Sdc4; Fgl2; Blvrb; Iglv1; Stmn1; Itsn1; Spsb1; Ust; Aspa; Ptms; Fggy; P2rx7; 1300002K09Rik; Plxna4; Slamf7; Dtx4; Capn3; Ntpcr; Slc16a6; Ston2; Phyhd1; B3galt5; H2-Ab1; Gdf15; Igj; Ttc28; Sec14l1; Clec4n; Mtss1; Arhgef12; Arhgap22; Enpp1; Wbp5; Cd69; Mcm6; Sesn1; Etv1; Pdgfa; Dmxl2; Nfxl1; Pld2; Pik3r1; Tspan33; Tmem176b; Fcgr4; Igkv4-55; Aoah; Serpinf1; Mir680-2; Sfmbt1 / ≥2.0
Mki67ip; Apoc1; Ccdc88c; Ctse; Ctse; Ctse; Ctse; Ctse; Ctse; Ctse; Rnf144a; Cnn2; Inhba; Sirpb1a; Cdc42ep2; Fam65b; 4930523C07Rik; Gyg; Pram1; Plp2; Agpat9; Tes; Plp2; Rab44; Pfkp; Klrb1f; Prtn3; Aim1; St3gal4; C3; 4930562F07Rik; Pyhin1; Stk10; Arhgap23; Plp2; Ggct; Lif; Ap1s2; Sort1; Nod1; Lrrk2; Adam8; Gm14005; Clec12a; Sirpb1a; Treml4; F13a1; Sirpb1b; Ear2; Ccnd3; Lyst; Fam129b; Spn; Irf7; Stom; Flna; Smpdl3a; Dna2; A530064D06Rik; Krt80; Zfyve9; Ass1; Serpinb2; Snora52; Snord33; Sirpb1b; Emilin2; Anxa2; Slc44a2; Fry; Gpr141; Tmem38b; Nxpe4; Ms4a4c; Tnfsf14; Asap1; Ass1; Ltb4r1; Ly6i; Slc2a6 / ≥3.0 / Card11; Antxr2; Rhoh; Fmn1; Igk-V21-2; Tsc22d1; Lphn3; Gm9001; Tbc1d4; Abcg3; Reps2; Ahrr; Lrp6; Nek6; Amica1; Fam213a; Tdgf1; 2900026A02Rik; Cspp1; Ly6a; Il18bp; Ciita; Prune2; Serpine1; Igl-V2; Dhrs3; Pon3; Lair1; Snx8; Bhlhe41; Scn1b; Fbxo32; Olfr161; Il1r2; Spic; Cd9; Pdcd1lg2; F11r; Ighv1-72; Sbf2; Rab3il1; Tmem26; Ephx1; Tgfbr1; Hrh1; Fcgrt; Rgl1; Itgb5; Bbs5; H2-DMb2; Cmtm8; Pdlim4; 1700047G07Rik; Slc13a3; Meis3; Tns1; Fblim1; Scimp; Gm16848; Sorbs3; Slco3a1; Slc29a1; Slamf6; B3galnt1; Hepacam2; Spred2; Cxcr3; D230041D01Rik; Ccdc23; Cpd; Eogt; 6720401G13Rik; Ocstamp; Sh3pxd2a; Ttyh2; LOC100504914; H2-Aa; Pdgfb; Ctla4; Igh-VJ558; Dmxl2; Gm11711; Zfp395; Snx24; Pea15a; Pltp; Il1a; P2ry14; Gm11711; Cd63; Tgfb3; Olfr111; Lrrc4c; Asb2; Tbxas1; Igkv4-71; Gpr157; Nuak1; Pdpn; Xlr; 1810011H11Rik; Axl; Pdgfc; Spred2; D8Ertd82e; Herpud1; Ifnb1; Timp2 / ≥3.0
Uck2; Camkk2; Emr4; Pi16; 5730408K05Rik; Hpse; Xylt1; Slc16a3; AB124611; Tiam1; Thbd; Grk5; Egln3; Taf1d; Adora2b; Fas; Pygl; Add3; Oas3; Akt3; Itpr1; Ms4a8a; Trem3; Ldlrad3; Hopx; Rasgrp2; Flt1; F5; Clec4e; Dgkg; Hdc; G0s2; Sepx1; Itgb7; Glipr2; Capg; S100a8 / ≥4.0 / Itgb5; Alox5; Wwp1; Itgav; Tm4sf5; Myc; G530011O06Rik; Procr; Tmem176a; Ccl22; Ppbp; Cd163; Ch25h; Ccnd1; Rcbtb2; Cpq; Fchsd2; Chst14; Spred1; Gna12; Ecm1; Pmp22; Mmp9; Art2b; Sash1; Rgs1; Abca1; Cd22; Igfbp4; Tlr1; Mvb12b; 4930506M07Rik; Gas6; Fnbp1l; Ccnd2; Pla2g2d; Frmd4b; C6; Cxcl1; Cxcl16; Agmo; Scamp5; Igk-V28; 8430419L09Rik; Psd3; Mgat4a; Etv5; Enpp4; Dip2c; Siglech; Fxyd2; Dst; Gpr171; Lpar1; Tns1 / ≥4.0
Saa3; Olr1; Tnfaip6; Cd177; Alox5ap; Sgms2; Gda / ≥5.0 / Chp2; LOC100046496; AW112010; Gpnmb; P2ry12; Loxl3; AI324046; Bmp2; Ttc28; Stk38l; Baiap2; Cd38; LOC672291; Hvcn1; Il12b; Gstm5; Timd4; Fmnl2; Il22ra2; Gdpd1; Creb5; Gpr31b; Zfp691 / ≥5.0
B3gnt5; Cdkn2d; Ifi205; Met; Trem1; Cdc42ep3; Napsa; Plcb1; Arg2 / ≥6.0 / Gpr31b; Folr2; Igf1; Rtn1; Rnf180; C3ar1; Gbp8; Abcc3; Tns1; BC055004; LOC435333; Ophn1; Cp; Igkv19-93; Zdhhc14; Hebp1; Amica1; Il7r; Dip2c; Kynu; Ltc4s; H2-Oa / ≥6.0
E230008N13Rik; Tarm1; Nfe2; Arhgap26; Lsp1; Gsr / ≥7.0 / Gbp4; Blnk; Tmem119; Slco2b1; Lag3; Mertk; Acp5; Il10; H2-Ob; Leprel1; Adam19; Mmp14; Tanc2 / ≥7.0
Arhgef37; Ly6c1; S100a4; E230008N13Rik; Ace / ≥8.0 / Dab2; Mmp12; Dip2c; Gm10134; Gatm; Lilra5; F630111L10Rik; Tm4sf19; Bank1; H2-Eb1; Mrc1; Ighm / ≥8.0
Ly6c2; Il6; Atp8b4 / ≥9.0 / Etv5; Tmem37; Slamf9; Fads1 / ≥9.0
Cd300lf; Chi3l1; Plac8; Mgst1 / ≥10.0 / Adamdec1; Ptgs1; Plau; Itgax; Myo1e; Spint1; Stab1; Mmp2 / ≥10.0
Slpi; Lilra6 / ≥11.0 / Kcnj10; P2ry13; Gpr34; Cadm1; Gpr114; Gbgt1 / ≥11.0
Slfn1; Slfn4 / ≥12.0 / Tanc2; Mgl2 / ≥12.0
E430024C06Rik; E430024C06Rik / ≥16.0 / Olfml3 / ≥13.0
1810033B17Rik / ≥17.0 / Ccl7; C1qc; Vcam1 / ≥15.0
F10 / ≥19.0 / Ms4a7; C1qb / ≥16.0
Fn1; Mmp8; Vcan / ≥20.0 / Ms4a14; Cd4; Pf4 / ≥18.0
Sell; Serpinb10 / ≥30.0 / Pmepa1; Npl / ≥19.0
Gm9733; Ifitm6; I830127L07Rik / ≥40.0 / Tlr12; Gbp1; Anpep; Cd81; Plxdc2; Sema6d; Itga9; Hpgds; H2-M2; Igk-V19-14 / ≥20.0
Hp / ≥50.0 / C1qa; Zmynd15; Klrb1b; Pgf; Pxdc1; Fcrls / ≥30.0
Chi3l3 / ≥100.0 / Ccl12; Cd72 / ≥40.0
Dnase1l3 / ≥50.0
Apol7c / ≥60.0
Ccl8; Mmp13 / ≥70.0

Supplemental Table 2: Comparison of the differentiation processes in colon and dermis

t-test: P1 vs P4; PRaw≤ 0.05; Fold Change ≥ 2.0 for dermis and colon respectively and identification of similarities and differences between the differentiation defining genes in the two organs.

Genes marked in red: 2-fold higher in colon P4 compared to dermis P4 (t-test: PRaw≤ 0.05; Fold change ≥ 2.0)

Downregulated from P1 to P4 / Upregulated from P1 to P4
Only Colon / Only Dermis / Colon + Dermis / Only Colon
2-fold higher compared to dermis / Only Dermis / Colon + Dermis
Sp100 / Il1r2 / Mki67ip / Pcmtd1 / Ly96 / Spred2
Ramp1 / Mir128-1 / Chd7 / Cspp1 / Il1rl1 / Sfmbt1
Zcchc2 / Nuak2 / E230008N13Rik / Gm10307 / Il18r1 / Mras
Serpinb2 / Cd244 / Itpr1 / Dst / Slc9a4 / Nrp2
Chi3l1 / Rnf149 / Taf1d / Il1r2 / Cd28 / Tnfrsf11a
4930523C07Rik / Ifngr1 / Sp110 / Il1rl2 / Adam23 / Il10
Trp53bp2 / Palm / Gpr35 / Stat4 / Acsl3 / 5430435G22Rik
Nab1 / Btg1 / Serpinb10 / Ctla4 / A530040E14Rik / F11r
Mfsd6 / Pde7b / Sell / Mroh2a / Slc35f5 / Slamf9
Csprs / Rassf3 / F5 / Sh2d1b1 / Fam72a / Mgat4a
Ppp1r15b / Gngt2 / Pyhin1 / Gm10522 / Rnasel / Tns1
Rgs18 / Kcnj2 / Fn1 / Fcgr4 / Glul / Tmem37
4930562F07Rik / Cd300a / Uck2 / 1700009P17Rik / 2810417H13Rik / Mcm6
Gm4955 / Rnf213 / Fabp7 / Slamf6 / 1110028C15Rik / Rgs1
Ifi205 / Cyfip2 / Smpdl3a / Kcnj10 / Per2 / Rgl1
Akt3 / Zfp39 / Ass1 / Kmo / Cfh / Npl
Lbr / Zkscan17 / Dna2 / Bpnt1 / Atp1b1 / Slamf7
Fbxo28 / Abi3 / Adora2a / Eprs / Sft2d2 / Pea15a
Ppp2r5a / Arl5c / Abca7 / Tmem206 / Fh1 / Arhgap18
G0s2 / Gpatch8 / Mdm1 / Mcm3 / Fam71a / Sesn1
H60b / Fam20a / Irak3 / 1110058L19Rik / Atf3 / Rhobtb1
Ctse / Hif1a / Lif / Prim2 / Rcor3 / Etv5
Herc4 / Siva1 / Bcl11a / Slc40a1 / Fbxo30 / Igf1
Prtn3 / Tspan13 / Stk10 / Lancl1 / Egr2 / Prim1
Cnn2 / Scarna13 / Adora2b / Usp37 / Dot1l / Cd63
Hmha1 / Gcnt2 / Slfn1 / Gpr55 / Fgd6 / Sash1
Arg1 / Tmem167 / Slfn4 / St8sia4 / Dusp6 / Gas2l3
Aim1 / Mier3 / Fmnl1 / Ralgps2 / Stxbp5 / Ap1b1
Dram1 / Sema4d / Ace / Ephx1 / Gpr126 / Adam19
Tmpo / Auh / Slc16a3 / Nenf / Prmt2 / Timd4
Esyt1 / Cdk7 / Arg2 / Il22ra2 / Slc41a2 / Pmp22
Osm / Rnase6 / Rnf144a / Trdn / Plxnc1 / Mgl2
Gnb2l1 / Lpar6 / Pygl / Tmem26 / Slc16a7 / Zmynd15
Zkscan6 / 5031414D18Rik / Ccdc88c / Ggt5 / Nudcd2 / Pld2
Atp2a3 / Gjb2 / Lyst / Ust / Kif3a / Adap2
Flot2 / Mir15a / Jarid2 / Tcf21 / Grap / Ccl7
Slfn5 / Gpr18 / Ccdc125 / Enpp1 / Snord118 / Ccl12
Arhgap23 / Nr4a1 / Gpr141 / Man1a / Asgr2 / Ccl8
Csf3 / Map3k12 / Nedd9 / Pald1 / Clec10a / Tanc2
Rara / Rnd1 / Agtpbp1 / Cdk1 / Aldoc / Ltc4s
Cd300lg / Heg1 / E430024C06Rik / Agpat3 / Ccl2 / Cxcl16
Sept9 / Gm608 / Vcan / Zfp938 / Ccl4 / Scimp
Tmc8 / Mefv / Itga1 / Appl2 / 4632419I22Rik / Gdpd1
Irgm1 / Srsf3 / Ltb4r1 / Nuak1 / Cnp / Abcc3
Slfn8 / Rrp1b / Dock5 / Spic / Atp6v0a1 / Abca9
Ccl9 / Zfp472 / Gramd4 / Dyrk2 / Tmem106a / Gm11711
Ccl6 / Myo1f / Lrrk2 / Dtx3 / Gprc5c / Trim47
Dusp3 / D330041H03Rik / Ly6i / Il23a / Mfsd11 / Etv1
Cd300lf / Lst1 / Ly6c1 / Pisd-ps1 / Birc5 / Ifi27l1
Tmc6 / Vegfa / Ly6c2 / Selm / Slc25a10 / Rtn1
Ccdc71l / Smchd1 / I830127L07Rik / Tbc1d10a / Rac3 / Galc
Adssl1 / Ttc39c / Abcd2 / Sh3pxd2b / Gm16516 / Lgmn
Pgk1 / Rnf125 / Bin2 / Il12b / Alox15 / Aoah
Pqlc3 / Malt1 / Itgb7 / Hs3st3a1 / Nlk / Gm7120
Stxbp6 / Ndst1 / Nfe2 / Tm4sf5 / Ccl5 / Pxdc1
Egln3 / Snhg1 / B3gnt5 / Mir212 / Ccl3 / Rnf180
Syne3 / Zfpl1 / Dgkg / Slc46a1 / Prr11 / Plau
Inhba / Prdx5 / Samsn1 / Copz2 / Nr1d1 / Rnase4
Fam65b / Gpd2 / Mx1 / Igfbp4 / Top2a / Zfp395
Emb / Itga4 / Sepx1 / 9930022D16Rik / Nt5c3b / Dnase1l3
Pfkp / Chst1 / Trem1 / Ttyh2 / Vat1 / Stab1
F13a1 / Lpcat4 / Trem3 / Sec14l1 / Gna13 / Sorbs3
1110007C09Rik / Thbs1 / Treml4 / C1qtnf1 / Exoc7 / Lacc1
Cast / Smox / Mocs1 / Gaa / Cbr2 / Tbc1d4
Plp2 / Mcts2 / Emr4 / Baiap2 / Snx13 / Sepp1
Gapt / 1110008F13Rik / Prkce / 0610009B22Rik / Syne2 / Dab2
Vcl / Cytip / Pot1b / Pdlim4 / Kcnk13 / Il7r
Tkt / Dpp4 / C3 / Ulk2 / Serpina3f / Mtss1
Ear2 / Gss / Emilin2 / Wsb2 / Rhob / Pdgfb
Spata13 / Tgm2 / Arhgap26 / Aspa / Prkar2b / Slc11a2
Irg1 / 4833422F24Rik / Arhgef37 / Hic1 / Hdac9 / Snx29
Ankrd28 / Atp11b / Rasgrp2 / Serpinf1 / Zfp36l1 / St6gal1
Ear1 / Lysmd1 / Ms4a4c / Cpd / Actn1 / Pigz
Ear10 / Ptpn22 / Grk5 / Xylt2 / Gpr68 / Tm4sf19
Gch1 / Camk2d / Cdc42ep2 / Cwc25 / Pitrm1 / Itsn1
Setdb2 / Fabp4 / Ms4a8a / Cd79b / Hist1h3a / Leprel1
Rgcc / Gm5150 / Gda / Pecam1 / Hist1h3g / St3gal6
Abcc4 / Dear1 / Tnfaip6 / Slc16a6 / Hist1h3d / Rcan1
Fbxo4 / Atp8b2 / Cers6 / Timp2 / Hist1h3b / Zdhhc14
Asap1 / Terc / Plcb1 / Agmo / Cmah / H2-DMb2
Tmem71 / I830077J02Rik / Slc2a6 / Eif2b2 / Irf4 / H2-Ab1
Plec / 6330407A03Rik / Nr4a2 / Tdp1 / Rreb1 / H2-Eb1
Nfam1 / 5730528L13Rik / Ldlrad3 / Pgf / Edn1 / Emr1
Lmbr1l / Kti12 / Atp8b4 / Tgfb3 / Cd83 / Mmp25
Krt80 / Slc2a1 / Slpi / Ston2 / Rnf144b / Decr2
Rarg / Rspo1 / Zbp1 / Asb2 / Slc12a7 / H2-Aa
Cyp2ab1 / Runx3 / Sort1 / Ighg / Arsb / D17H6S56E-5
Alcam / Prdm2 / Gm9733 / AI324046 / Plk2 / Tnf
Tiam1 / N4bp2 / Sirpb1a / Igh-VJ558 / Hist1h3i / H2-M2
Tiam2 / Cds1 / Sirpb1b / Ighm / Hist1h3e / Map4k3
Agpat4 / Setd8 / Chi3l3 / Ighv1-72 / Hist1h3c / Dmxl1
Sod2 / Bri3bp / Sgms2 / LOC435333 / Tubb2a / Cd74
Rab44 / Plod3 / Glipr2 / Dip2c / Tbc1d7 / Spire1
Pi16 / C130050O18Rik / Tmem38b / Mylip / Atxn1 / Slc14a1
Cyp4f16 / Pilrb1 / Csf3r / Rmi1 / Hk3 / Rab3il1
Pram1 / Irak2 / Fgr / Lpcat1 / Slc35d2 / Fads1
Cyp39a1 / Necap1 / Id3 / Tppp / Rasa1 / Prune2
Ccnd3 / Clec2i / E2f2 / Mef2c / Gfra2 / Ms4a14
B430306N03Rik / Cdkn1b / Padi2 / Akr1e1 / Ccdc122 / Ms4a7
2410091C18Rik / Cmas / Nadk / Serpinb6a / Ear11 / Ch25h
Foxn2 / Il12rb2 / Megf9 / Gkap1 / Slc7a8 / Blnk
Fkbp5 / Snora7a / Zfyve9 / Ctsl / 6330409N04Rik / 4930506M07Rik
A530064D06Rik / Klrk1 / Padi4 / Ahrr / Ints6 / Mrc1
Tnfsf14 / Klra2 / Gm1673 / Jmy / Ednrb / Gbgt1
Cdc42ep3 / Magohb / Agpat9 / Pik3r1 / Gpr183 / Gm10134
Haao / Plbd1 / Tmem156 / Flnb / Lifr / Ralgds
Rsl24d1 / Ldhb / Hopx / 1810011H11Rik / Maff / Nek6
Mocos / 5730419I09Rik / Plac8 / Arhgap22 / Sept3 / Acp2
Eno1 / Pglyrp1 / Oas3 / Mmp14 / Parvb / Fmn1
Impa2 / Rras / Scarb1 / Kif13b / Slc48a1 / Spred1
Diap1 / Taldo1 / Flt1 / Rcbtb2 / Tmem106c / Sema6d
Me2 / Apoc2 / Met / Tsc22d1 / Stk3 / Mertk
Fosl1 / Ceacam1 / Il17ra / Plac9 / Ift27 / Mmp9
Trmt112 / Eed / Scnn1a / Fam213a / A4galt / Dpp7
Ahnak / Coro1a / Klrb1f / Adamdec1 / Lmf2 / Uap1l1
Ms4a4b / Tnfrsf26 / Mgst1 / Rnf219 / Smagp / Gpr155
Rcl1 / D230025D16Rik / Tmsb10 / C6 / Mucl1 / Ctnnd1
Fas / Atmin / Clec4e / Cpq / Tnfrsf17 / B230118H07Rik
Slk / Rab11fip1 / Ptgir / Dcstamp / Abcc1 / Gatm
Add3 / Nrg1 / Map4k1 / Col14a1 / Tfrc / Il1a
5730408K05Rik / Rbpms / Napsa / Myc / Osbpl11 / Mafb
Stx3 / Cd97 / Xylt1 / Pvt1 / Naa50 / Sdc4
Anxa1 / Ddx28 / Itgal / Grasp / Cd200r1 / Pltp
Sgms1 / Gcsh / Cd177 / Basp1 / Retnla / Slc13a3
Avpi1 / Slc25a20 / Atp1a3 / Fbxo32 / Pros1 / Nfatc2
Fam129b / Oaf / Gm1966 / Ly6a / 2810055G20Rik / Mir1956
Snai1 / Ibtk / Spn / Apol7c / Il10rb / P2ry14
Ptpn1 / Rbm15b / Ifitm3 / Olfr161 / Slc35a5 / P2ry13
Lcn2 / Ifitm6 / Ciita / Snx9 / P2ry12
Traf1 / 1810033B17Rik / Hes1 / Tmem8 / B3galnt1
Stom / F10 / Itgb5 / Hspa1a / Fcrls
Sestd1 / Gsr / Cd200r4 / Ly6g6c / Ecm1
Hdc / Plcg2 / Mir99a / Ppp1r10 / Cttnbp2nl
Gm14005 / Rhou / Ttc3 / Trem2 / Fnbp1l
Gpcpd1 / Ikbkb / B3galt5 / Rasgrp3 / Bank1
Thbd / Klhl2 / Slc7a4 / Heatr5b / Smc2
Samhd1 / Hp / Iglv1 / Galm / Ccdc163
Elmo2 / Mmp8 / Igl-V2 / Tmx2 / Stmn1
Helz2 / Slc44a2 / Tulp4 / Tnfrsf12a / Pla2g2d
Isg20l2 / Ldlr / Syngap1 / Nme4 / Dhrs3
S100a4 / Nxpe4 / Fgd2 / C4b / Wwp1
S100a6 / Rab27a / H2-Oa / Tubb5 / Cd72
S100a8 / Cdkn2d / H2-Ob / Fez2 / Abca1
S100a10 / Sorl1 / Olfr111 / Cables1 / Ttc39b
Pgam1 / 2610018G03Rik / Tbcc / Impact / Ifnb1
Gyg / Mbnl3 / Epb4.1l3 / Tslp / Man1c1
Kpna2 / Gyk / 1110001A16Rik / Commd10 / C1qb
Slc22a15 / Gpr31b / Snx2 / C1qc
Chi3l4 / Fpr1 / Gm4951 / C1qa
Alpk1 / Prss30 / B4galt6 / Fblim1
Ripk2 / Slc9a3r2 / Hbegf / Fam213b
Tstd3 / Aif1 / Aldh7a1 / Abcb1b
Mob3b / Enpp4 / Haus1 / Cd38
Coro2a / Slc29a1 / Fibp / Ppbp
Smpdl3b / Cystm1 / Ifit1 / Pf4
Pgd / Hsd17b4 / Vegfb / Cxcl1
Kcnab2 / Snx24 / Gcnt1 / Cxcl13
Il6 / Iigp1 / Mamdc2 / Hvcn1
Mrpl33 / Smad7 / Lipo1 / P2rx7
Bst1 / Prelid2 / Myof / BC055004
Lrrc8b / 4930503L19Rik / Rbp4 / Cd36
Crybb1 / Ctsf / Il1rn / Nfxl1
Oasl2 / Fads3 / Tank / Cxcl10
Slc24a6 / Cd274 / Itga6 / Rasgef1b
Alox5ap / Pdcd1lg2 / Slc28a2 / Pdgfa
Fry / Fam178a / AA467197 / Snx8
Gm10268 / AW112010 / Blvra / Gna12
Prkag2 / Dtx4 / Ptpra / Tmem140
Fbxl5 / Fam189a2 / Mavs / Tmem176a
LOC100505155 / Insl6 / Cbfa2t2 / Creb5
Spink2 / Arhgap19 / Epb4.1l1 / Hrh1
Naaa / Sh3pxd2a / Ube2c / Clec4b1
Hpse / Plxdc2 / Pfkfb3 / Cd163
Mfsd7a / Phyhd1 / Fcna / Hepacam2
Unc119b / Ptgs1 / Gtf3c5 / Pon3
Oas2 / Kynu / Stxbp1 / Fam3c
Aldh2 / Fmnl2 / Rnd3 / Tmem176b
Camkk2 / Bbs5 / Arhgap11a / Hpgds
Ccl24 / Dusp19 / Ehd4 / Rab11fip5
n-R5s180 / Itgav / Slc30a4 / Eogt
Tes / Rapsn / Siglec1 / Frmd4b
Zyx / Lrrc4c / Slc23a2 / Camk1
Chn2 / Ccdc34 / Flrt3 / Alox5
Ndnf / Chst14 / Cd93 / C3ar1
Capg / Spint1 / Sulf2 / Cd4
Clec4d / Capn3 / Gpr160 / Lag3
Clec12a / Dut / Spg20 / Klrb1b
Samd9l / Bmp2 / Selenbp2 / D230041D01Rik
Gm4876 / Srxn1 / Selenbp1 / Hebp1
Nod1 / Procr / Hist2h2be / Lilra5
Ggct / Src / Hist2h3c1 / Blvrb
Gadd45a / Inpp5e / Hist2h3b / Cebpa
Olr1 / Fnbp1 / Bcar3 / Siglech
Eps8 / Mvb12b / Mcoln2 / Mtmr10
Rasgrp4 / Tfpi / Sclt1 / Fchsd2
Dmkn / Plcb2 / Nhlrc3 / Swap70
Atp10a / 1500011K16Rik / Pmf1 / Chp2
Isg20 / Acss1 / S100a1 / Itgax
Ampd3 / Soga1 / Snx27 / Tspan4
Snora52 / Ada / S1pr1 / Cd81
Lsp1 / Ocstamp / Enpep / Fosb
Pira11 / Pmepa1 / Tmem64 / Scn1b
Pira1 / Cp / Tmod1 / Cd33
Lilra6 / Nceh1 / Slc44a1 / Siglece
Apoc1 / Pdgfc / Tmem48 / Fcgrt
Bcl3 / Pmvk / Mobkl2c / Slco2b1
Lsr / Lix1l / Fhl3 / Folr2
Snord33 / Rhoc / Plekhg5 / Tpp1
Saa3 / Adora3 / Fam132a / Sbf2
Dgat2 / Gstm5 / Atp6v0d2 / Itpripl2
A530023O14Rik / Gbp1 / Jun / Mki67
Lmo1 / Gpr171 / 1110049F12Rik / D8Ertd82e
Nupr1 / F630111L10Rik / Kif1b / Ccl22
Adam8 / Rapgef2 / Cxcl3 / Cd209f
Rnh1 / Lmna / Areg / Gas6
Irf7 / Bcl9 / Anxa3 / Psd3
Myadm / Fam46c / 4930524J08Rik / Gdf15
Ppp2cb / Olfml3 / Oasl1 / Arhgap10
Nod2 / Vcam1 / Gpr146 / Mmp13
Ankrd37 / Dnajb4 / Tnip2 / Mmp12
Piezo1 / 1300002K09Rik / Tec / Fxyd2
Cbfa2t3 / Tgfbr1 / Ube2n / Cadm1
AB124611 / Fggy / Cmklr1 / Myo1e
Pstpip1 / Ccdc23 / Trpv4 / Slc9a9
Pkm / Camk2n1 / Ccl24 / Itga9
Vps13c / Gpr157 / Mepce / Slc37a2
Anxa2 / AI427809 / Akr1b8 / Scamp5
Cish / Lpar1 / Rny3 / Tgfbr2
Ccr2 / Cdk5rap2 / Mpp6 / Gpr34
St3gal4 / Ipo13 / Aqp1 / Ocrl
Nbeal2 / Zfp691 / Mad2l1 / Stard8
Myd88 / Ermap / Retsat / Wbp5
Tarm1 / Tlr12 / Mitf / Tceal1
Styx / Pdpn / Cdca3 / Xlr
A630033H20Rik / Spsb1 / C530028O21Rik / Renbp
Diap2 / Fgl2 / Clec2d / Ophn1
Map3k15 / Rbpj / Emp1 / Cxcr3
Ap1s2 / Tbc1d19 / Samd9l / Tspyl2
Sept6 / Rhoh / Glcci1 / Reps2
C1galt1c1 / Lphn3 / Tfec / Plekhn1
Sms / Ttc28 / Wdr91
Flna / LOC100504914 / Clec5a
G6pdx / Adam22 / Tpk1
Prkx / Gm5129 / Gimap6
Tlr1 / Dfna5
Igj / Exoc6b
Antxr2 / 1700040I03Rik
Wdfy3 / Ncapd2
Abcg3 / Eps8
Gbp8 / Lig1
Gbp4 / Pepd
Mpa2l / Zfp719
2900026A02Rik / Prc1
Tmem119 / Pak1
Serpine1 / Styx
Card11 / Wee1
Stard13 / Rbbp6
Tspan33 / Cd151
Akr1b10 / Ap2a2
Tbxas1 / Dhcr7
Gpnmb / Rnf141
Abcg2 / C5ar1
Serbp1 / Kcnk6
Igk-V28 / Idh2
Igk / l7Rn6
Loxl3 / Rnf169
8430410A17Rik / P2ry6
Clec4n / Lyve1
C1ra / Gprc5b
8430419L09Rik / Cdr2
Stk38l / Sult1a1
Plxna4 / Cox6a2
Pdia4 / Dusp8
Rarres2 / Cd209g
LOC672291 / Cln8
Igkv19-93 / Dusp4
Igkv4-71 / Ddx60
Igkv4-55 / Lpl
Gm16848 / Slc27a1
Igk-V19-14 / Syce2
Igk-V21-2 / Ccl17
Gm9001 / Gpr56
Hk2 / Cmtm3
Actg2 / Pla2g15
Wnk1 / Clec4g
Ptms / Cd209a
Cd9 / Cd209e
Ccnd2 / Cd209d
Cd69 / Cd209b
Lrp6 / 2410022L05Rik
Bhlhe41 / Adam9
Zfp667 / Tmem184c
Meis3 / Maf
Tmem86a / Siae
Tubgcp5 / 1600029D21Rik
Sema4b / Snord16a
Akip1 / Myo5a
Pde3b / Cd109
Eef2k / Bcl2a1a
Il21r / Bcl2a1b
Bag3 / Hyal1
Htra1 / Nat6
Ifitm1 / Bcl2a1c
Tspan32 / Tmem205
Tssc4 / Anln
Lair1 / Gm6762
Tnni3 / Mpi
Rasl2-9 / Coro2b
Apoe / Fem1b
Axl / Ccnb2
Pld3 / Bcl2a1d
Zfp780b / Dnajc13
Cd22 / Ano10
Rcn3 / Maoa
Slco3a1 / Slc6a8
Anpep / F630028O10Rik
Tsku / P2ry10
Art2b / Cfp
Il18bp / Dnase1l1
Hbb-b2 / Taf9b
St5 / Cysltr1
Vkorc1 / Ptchd1
Rgs10 / Car5b
Ccnd1
Tnfsf13b
Mfhas1
Aga
Inpp4b
Mmp2
Lpcat2
Capns2
Mt2
Mt1
Herpud1
Cpne2
Gpr114
1700047G07Rik
Zfhx3
Irf8
Ntpcr
Tlr3
Zcchc14
Kbtbd3
Sesn3
Bbs9
Clmp
Amica1
Myo9a
Uaca
Fam214a
Nicn1
Vipr1
Acp5
Zfp810
Arhgef12
1110032A03Rik
Dmxl2
Cd276
Fam212a
Klhl18
Tdgf1
Cmtm8
Cx3cr1
Cxx1c
Ngfrap1
Nxt2
Mir680-2
Mid1
Dppa3
6720401G13Rik
Maged1
G530011O06RIK
A730008H23Rik

Supplemental Table 3: Gene Set Enrichment Analysis

GSEA analysis of the genes changed by at least 2-fold during the differentiation from P1 to P4 in the colon. (KEGG Database)

Pathway / Genes / Statistics
Cytokine-cytokine receptor interaction / Il22ra2; Bmp2; Il10; Ccl7; Pdgfc; Pdgfa; Osm; Ccl22; Ifnb1; Cxcl1; Cxcr3; Tnfrsf1b; Cx3cr1; Il17ra; Pdgfb; Cxcl14; Cxcl10; Tnfsf14; Flt1; Csf3r; Il6ra; Cxcl9; Tgfbr2; Ccl9; Met; Ccl6; Lif; Il7r; Cxcl16; Inhba; Ccr7; Tnfrsf11a; Tgfb3; Il6; Ccl24; Fas; Il1r2; Il1a; Tgfbr1; Ppbp; Il21r; Tnf; Csf3; Ccl17; Tnfsf13b; Ccr2; Flt3; Il12b; Pf4 / rawP=3.97e-18;adjP=5.60e-16
Celladhesionmolecules (CAMs) / Vcan; F11r; Icam2; Sell; H2-Eb1; H2-Aa; H2-DMb2; Pdcd1lg2; H2-M2; Ctla4; Itgb2; Sdc4; H2-Ob; Itgb7; H2-Oa; H2-DMa; Cd22; Cd4; Pecam1; Spn; Cd274; Itga6; H2-T24; Cadm1; Vcam1; Alcam; H2-Ab1; Itgav; Itgal; Itga9 / rawP=9.41e-12;adjP=6.63e-10
Staphylococcusaureusinfection / C3ar1; Il10; C5ar1; H2-Eb1; H2-Aa; H2-DMb2; Itgb2; C1qc; H2-Ob; H2-Oa; C1qa; H2-DMa; Fpr1; C1qb; Fcgr4; H2-Ab1; Itgal / rawP=1.59e-11;adjP=7.47e-10
Rheumatoid arthritis / Pgf; Acp5; H2-Eb1; H2-Aa; Tnfrsf11a; H2-DMb2; Ctla4; Tgfb3; Itgb2; Il6; Tlr2; H2-Ob; H2-Oa; Il1a; H2-DMa; Tnf; Ctsl; Tnfsf13b; Flt1; H2-Ab1; Itgal / rawP=2.34e-10;adjP=8.25e-09
Malaria / Csf3; Tnf; Il10; Met; Pecam1; Myd88; Cd81; Cd36; Vcam1; Itgb2; Tgfb3; Il6; Tlr2; Sdc4; Itgal / rawP=6.23e-10;adjP=1.76e-08
Chagasdisease (American trypanosomiasis) / Il10; Ace; Pik3r1; Plcb1; Ifnb1; Tgfb3; Ikbkb; Il6; C1qc; Tlr2; Fas; Plcb2; C1qa; Tgfbr1; Tnf; Ppp2cb; C1qb; Myd88; Akt3; Serpine1; Tgfbr2; Il12b / rawP=2.89e-09;adjP=6.79e-08
Hematopoieticcelllineage / Itga1; Il7r; H2-Eb1; Cd36; Il6; Il1r2; Il1a; Anpep; Tnf; Csf3; Cd22; Cd33; Cd4; Cd38; Itga6; Csf3r; Il6ra; Flt3; Cd9 / rawP=8.21e-09;adjP=1.65e-07
Leishmaniasis / Tnf; Il10; Myd88; H2-Eb1; H2-Aa; H2-DMb2; Fcgr4; Tgfb3; Itgb2; H2-Ab1; Tlr2; Il12b; H2-Ob; H2-Oa; Il1a; H2-DMa / rawP=3.99e-08;adjP=7.03e-07
MAPK signalingpathway / Pdgfa; Gna12; Prkx; Rapgef2; Gadd45g; Ikbkb; Nr4a1; Rasgrp4; Pdgfb; Map2k3; Stmn1; Akt3; Mras; Tgfbr2; Flnb; Map4k1; 2010110P09Rik; Rasgrp2; Stk4; Myc; Mef2c; Tgfb3; Fas; Daxx; Gadd45a; Nfatc2; Pla2g2d; Il1r2; Il1a; Tgfbr1; Tnf; Map4k3; Flna; Dusp3; Rasgrp1 / rawP=9.05e-08;adjP=1.39e-06
Chemokinesignalingpathway / Rasgrp2; Ccl9; Ccl6; Ccl7; Cxcl16; Ccr7; Pik3r1; Prkx; Ccl22; Plcb1; Ikbkb; Cxcl1; Cxcr3; Ccl24; Tiam1; Grk5; Plcb2; Cx3cr1; Ppbp; Ccl17; Cxcl14; Cxcl10; Ccr2; Fgr; Akt3; Cxcl9; Pf4 / rawP=9.87e-08;adjP=1.39e-06
Toxoplasmosis / Alox5; Il10; Ldlr; H2-Eb1; H2-Aa; H2-DMb2; Pik3r1; Tgfb3; Ikbkb; Tlr2; H2-Ob; Pla2g2d; H2-Oa; H2-DMa; Tnf; Ciita; Map2k3; Myd88; Itga6; Akt3; H2-Ab1; Il12b / rawP=1.22e-07;adjP=1.43e-06
Graft-versus-host disease / Tnf; H2-Eb1; H2-Aa; H2-DMb2; H2-T24; H2-M2; Il6; H2-Ab1; Fas; H2-Ob; H2-Oa; Il1a; H2-DMa / rawP=1.20e-07;adjP=1.43e-06
Allograftrejection / Tnf; Il10; H2-Eb1; H2-Aa; H2-DMb2; H2-T24; H2-M2; H2-Ab1; Fas; H2-Ob; Il12b; H2-Oa; H2-DMa / rawP=1.63e-07;adjP=1.77e-06
Asthma / Tnf; Il10; H2-Eb1; H2-Aa; H2-DMb2; H2-Ab1; H2-Ob; H2-Oa; H2-DMa / rawP=5.86e-07;adjP=5.90e-06
Antigen processingandpresentation / Tnf; Ciita; Ctsl; Cd4; Lgmn; H2-Eb1; H2-Aa; H2-DMb2; H2-T24; H2-M2; H2-Ab1; H2-Ob; Cd74; H2-Oa; H2-DMa / rawP=9.84e-07;adjP=9.25e-06
Type I diabetes mellitus / Tnf; H2-Eb1; H2-Aa; H2-DMb2; H2-T24; H2-M2; H2-Ab1; Fas; H2-Ob; Il12b; H2-Oa; Il1a; H2-DMa / rawP=1.07e-06;adjP=9.43e-06
Intestinal immune network for IgA production / Il10; Tnfsf13b; H2-Eb1; H2-Aa; H2-DMb2; Il6; H2-Ab1; H2-Ob; H2-Oa; Itgb7; H2-DMa / rawP=2.44e-06;adjP=1.94e-05
Systemiclupuserythematosus / Tnf; Il10; C1qb; H2-Eb1; H2-Aa; H2-DMb2; Fcgr4; H2-Ab1; C1qc; H2-Ob; H2-Oa; C6; C1qa; H2-DMa / rawP=2.48e-06;adjP=1.94e-05
Amoebiasis / Il10; 5430435G22Rik; Pik3r1; Prkx; Plcb1; Serpinb10; Itgb2; Tgfb3; Il6; Tlr2; Fn1; Plcb2; Il1r2; Tnf; Vcl; Serpinb6a; Serpinb2; Arg2; Il12b / rawP=3.35e-06;adjP=2.49e-05
African trypanosomiasis / Tnf; Il10; Myd88; Plcb1; Vcam1; Il6; Fas; Il12b; Plcb2 / rawP=8.55e-06;adjP=6.03e-05
Phagosome / 5430435G22Rik; Mrc1; Itgb5; H2-Eb1; H2-Aa; Cd36; H2-DMb2; H2-M2; Cd209f; Itgb2; Tlr2; Olr1; H2-Ob; H2-Oa; H2-DMa; Scarb1; Ctsl; Coro1a; H2-T24; Fcgr4; H2-Ab1; Itgav / rawP=1.07e-05;adjP=7.18e-05
Autoimmune thyroiddisease / Il10; H2-Eb1; H2-Aa; H2-DMb2; H2-T24; H2-M2; Ctla4; H2-Ab1; Fas; H2-Ob; H2-Oa; H2-DMa / rawP=2.31e-05;adjP=0.0001
Toll-like receptor signaling pathway / Tlr3; Pik3r1; Ifnb1; Ikbkb; Il6; Tlr2; Lbp; Tlr1; Tnf; Cxcl10; Map2k3; Myd88; Akt3; Cxcl9; Il12b; Irf7 / rawP=2.46e-05;adjP=0.0001
Focal adhesion / Itga1; Pgf; Met; Diap1; Itgb5; Pdgfc; Pdgfa; Pik3r1; Ccnd3; Fn1; Itgb7; Ccnd2; Ccnd1; Pdgfb; Vcl; Itga6; Flna; Flt1; Igf1; Akt3; Zyx; Itgav; Flnb; Itga9; Src / rawP=2.26e-05;adjP=0.0001
Jak-STAT signaling pathway / Spred1; Il22ra2; Il10; Il7r; Lif; Myc; Osm; Stat4; Pik3r1; Ifnb1; Il6; Ccnd3; Ccnd2; Spred2; Ccnd1; Il21r; Csf3; Csf3r; Il6ra; Akt3; Il12b / rawP=1.69e-05;adjP=0.0001
Complement and coagulation cascades / C3ar1; Plau; C1qb; C5ar1; Thbd; Serpine1; C1qc; F5; Tfpi; C6; F10; F13a1; C1qa / rawP=3.73e-05;adjP=0.0002
Metabolic pathways / Alox5; Tk1; Pmvk; Plcb1; Dgka; Pfkp; Plcb2; Aldoc; Ggt5; Man1c1; Man1a; Adssl1; St6gal1; Xylt1; Kynu; Inpp4b; St3gal4; Pla2g7; Hpse; Bst1; Nadk; Dgat2; Lpcat4; Pla2g2d; Lpcat2; Pld2; Mgat4a; Ntpcr; Ltc4s; St3gal6; Pgk1; Haao; Hsd17b4; Ada; Agpat4; C1galt1c1; Ampd3; Hpgds; Ass1; Gaa; Gch1; Glud1; Dhrs3; Impa2; Plcg2; Sgms2; B3gnt5; Idh2; Cd38; Ptgs1; Dgkg; Pkm; Gyk; Agpat9; Arg2; Gatm; Dnmt3a; Gda; Hk2; Auh; Gns; Galc; Pon3; Gbgt1; Glul; Pgd; Cbr2; B3galnt1; Anpep; Agpat3; Aldh2; G6pdx; Pgam1; Uap1l1; Ocrl; B3galt5; Hdc; Eprs; Lpcat1; Tkt; Sgms1; Tbxas1; Uck2; Enpp1; Upp1 / rawP=3.65e-05;adjP=0.0002
B cell receptor signaling pathway / 2010110P09Rik; Plcg2; Cd22; Cd72; Cd81; Blnk; Pik3r1; Akt3; Cd79b; Ikbkb; Card11; Nfatc2; Ifitm1 / rawP=6.89e-05;adjP=0.0003
Hypertrophic cardiomyopathy (HCM) / Tnf; Itga1; Ace; Itgb5; Itga6; Lmna; Igf1; Prkag2; Tgfb3; Tnni3; Il6; Itgav; Itgb7; Itga9 / rawP=5.94e-05;adjP=0.0003
Osteoclast differentiation / Mitf; Acp5; Tnfrsf11a; Blnk; Pik3r1; Ifnb1; Ikbkb; Il1a; Tgfbr1; Tnf; Fosb; Plcg2; Akt3; Fcgr4; Fosl1; Tgfbr2; Lilra6 / rawP=6.78e-05;adjP=0.0003
Lysosome / Sort1; Lgmn; Gns; Acp5; Galc; Ctse; Cd63; Gaa; Tpp1; Ctsf; Ap1s2; Ctsl; Acp2; Ap1b1; Slc11a2; Aga; Napsa / rawP=0.0001;adjP=0.0005
Pathways in cancer / Bmp2; Mitf; Pgf; Met; Stk4; Mmp9; Myc; Pdgfa; Pik3r1; Tgfb3; Ikbkb; Il6; Traf1; Fas; Fn1; Rara; Mmp2; Egln3; Ccnd1; Tgfbr1; Pdgfb; Ralgds; Plcg2; Itga6; Csf3r; Igf1; Akt3; Flt3; Cebpa; Itgav; Tgfbr2 / rawP=0.0003;adjP=0.0013
Glutathione metabolism / Ggt5; G6pdx; Gstm5; Idh2; Mgst1; Gsr; Ggct; Pgd; Anpep / rawP=0.0004;adjP=0.0017
NOD-like receptor signaling pathway / Tnf; Nod1; Naip2; Ripk2; Cxcl1; Ikbkb; Il6; Nod2; Pstpip1; Mefv / rawP=0.0004;adjP=0.0017
Viral myocarditis / H2-Eb1; H2-Aa; H2-DMb2; H2-T24; H2-M2; Itgb2; H2-Ab1; H2-Ob; H2-Oa; Itgal; Ccnd1; H2-DMa / rawP=0.0007;adjP=0.0028
Regulation of actin cytoskeleton / Itga1; Diap1; Itgb5; Arhgef12; Pdgfc; Pdgfa; Gna12; Pik3r1; Itgb2; Tiam1; Fn1; Itgb7; Itgax; Pdgfb; Vcl; Itga6; Mras; Itgav; Baiap2; Itgal; Diap2; Itga9 / rawP=0.0009;adjP=0.0035
Dilatedcardiomyopathy / Tnf; Itga1; Itgb5; Itga6; Prkx; Lmna; Igf1; Tnni3; Tgfb3; Itgav; Itgb7; Itga9 / rawP=0.0016;adjP=0.0059
Priondiseases / Il6; C1qc; C1qb; C6; Il1a; C1qa; Prkx / rawP=0.0016;adjP=0.0059
Carbohydratedigestionandabsorption / Akt3; Hk2; Plcb2; Fxyd2; Pik3r1; Atp1b3; Atp1a3 / rawP=0.0027;adjP=0.0098
Bilesecretion / Scarb1; Ldlr; Abcc3; Nceh1; Fxyd2; Prkx; Ephx1; Abcg2; Atp1a3; Atp1b3 / rawP=0.0030;adjP=0.0106
TGF-beta signalingpathway / Tnf; Bmp2; Ppp2cb; Zfyve9; Myc; Inhba; Id3; Smad7; Tgfb3; Tgfbr2; Tgfbr1 / rawP=0.0031;adjP=0.0107
Natural killer cell mediated cytotoxicity / Tnf; 2010110P09Rik; Plcg2; Icam2; Pik3r1; Fcgr4; Cd244; Ifnb1; Sh2d1b1; Itgb2; Fas; Nfatc2; Itgal / rawP=0.0038;adjP=0.0128
Glycerolipid metabolism / Agpat4; Aldh2; Dgat2; Dgkg; Dgka; Gyk; Agpat9; Agpat3 / rawP=0.0039;adjP=0.0128
Phosphatidylinositol signaling system / Impa2; Ocrl; Plcg2; Itpr1; Pik3r1; Plcb1; Dgkg; Dgka; Inpp4b; Plcb2 / rawP=0.0041;adjP=0.0131
Endocytosis / Zfyve9; Met; Ldlr; Folr2; Rab11fip1; H2-M2; Tgfb3; Psd3; Grk5; Tgfbr1; Pld2; Fam125b; H2-T24; Flt1; Smad7; Dab2; Wwp1; Tgfbr2; Src; Asap1 / rawP=0.0044;adjP=0.0138
Glycerophospholipid metabolism / Agpat4; Lpcat4; Lpcat1; Dgkg; Dgka; Agpat9; Pla2g2d; Lpcat2; Agpat3; Pld2 / rawP=0.0049;adjP=0.0150
p53 signaling pathway / Sesn1; Igf1; Serpine1; Gadd45g; Fas; Ccnd3; Gadd45a; Ccnd2; Ccnd1 / rawP=0.0053;adjP=0.0159
Ether lipid metabolism / Lpcat1; Pla2g7; Lpcat4; Pla2g2d; Lpcat2; Pld2 / rawP=0.0057;adjP=0.0167
Aldosterone-regulated sodium reabsorption / Slc9a3r2; Fxyd2; Scnn1a; Pik3r1; Atp1b3; Igf1; Atp1a3 / rawP=0.0063;adjP=0.0181
ABC transporters / Abca7; Abca9; Abca1; Abcc3; Abcg2; Abcg3; Abcd2 / rawP=0.0071;adjP=0.0200
Melanoma / Pdgfb; Mitf; Met; Pdgfc; Pdgfa; Pik3r1; Igf1; Akt3; Ccnd1 / rawP=0.0079;adjP=0.0210
Acute myeloid leukemia / Akt3; Ikbkb; Flt3; Cebpa; Myc; Rara; Ccnd1; Pik3r1 / rawP=0.0077;adjP=0.0210
Pancreatic cancer / Pgf; Ralgds; Pik3r1; Akt3; Ikbkb; Tgfb3; Tgfbr2; Ccnd1; Tgfbr1 / rawP=0.0079;adjP=0.0210
Apoptosis / Tnf; 2010110P09Rik; Myd88; Pik3r1; Prkx; Akt3; Ikbkb; Irak3; Fas; Il1a / rawP=0.0091;adjP=0.0238
Salivary secretion / Cd38; Itpr1; Fxyd2; Prkx; Plcb1; Plcb2; Atp1a3; Bst1; Atp1b3 / rawP=0.0095;adjP=0.0244
Pentose phosphate pathway / Tkt; G6pdx; Pgd; Pfkp; Aldoc / rawP=0.0106;adjP=0.0262
Adherens junction / Vcl; Snai1; Met; Ptpn1; Tgfbr2; Ctnnd1; Baiap2; Tgfbr1; Src / rawP=0.0104;adjP=0.0262
Vascular smooth muscle contraction / Arhgef12; Adora2a; Gna12; Itpr1; Prkx; Plcb1; Adora2b; Ptgir; Plcb2; Pla2g2d; Ramp1; Prkce / rawP=0.0113;adjP=0.0275
Riboflavin metabolism / Acp2; Acp5; Enpp1 / rawP=0.0119;adjP=0.0284
Colorectal cancer / Ralgds; Myc; Pik3r1; Akt3; Tgfb3; Tgfbr2; Ccnd1; Tgfbr1 / rawP=0.0139;adjP=0.0327
Leukocyte transendothelial migration / Vcl; F11r; Rhoh; Plcg2; Mmp9; Pecam1; Pik3r1; Vcam1; Itgb2; Ctnnd1; Mmp2; Itgal / rawP=0.0147;adjP=0.0340
Proximal tubule bicarbonate reclamation / Glud1; Fxyd2; Atp1b3; Atp1a3 / rawP=0.0166;adjP=0.0374
Hepatitis C / Tnf; Ppp2cb; Scarb1; Ldlr; Tlr3; Oas2; Cd81; Pik3r1; Akt3; Ifnb1; Ikbkb; Oas3; Irf7 / rawP=0.0167;adjP=0.0374
GnRH signaling pathway / Mmp14; Map2k3; Itpr1; Prkx; Plcb1; Mmp2; Plcb2; Pla2g2d; Pld2; Src / rawP=0.0181;adjP=0.0399
Alanine, aspartate and glutamate metabolism / Ass1; Glul; Adssl1; Glud1; Aspa / rawP=0.0188;adjP=0.0402
T cell receptor signaling pathway / Tnf; 2010110P09Rik; Il10; Cd4; Pik3r1; Akt3; Ctla4; Ikbkb; Card11; Nfatc2; Rasgrp1 / rawP=0.0186;adjP=0.0402
Glycolysis / Gluconeogenesis / Pkm; Pgk1; Aldh2; Pgam1; Hk2; Pfkp; Aldoc / rawP=0.0206;adjP=0.0434
Small cell lung cancer / Akt3; Ikbkb; Traf1; Itgav; Fn1; Myc; Itga6; Ccnd1; Pik3r1 / rawP=0.0229;adjP=0.0468
ECM-receptor interaction / Itga1; Itgb5; Itga6; Cd36; Itgav; Sdc4; Fn1; Itgb7; Itga9 / rawP=0.0229;adjP=0.0468
Primary immunodeficiency / Ciita; Il7r; Cd4; Ada; Blnk / rawP=0.0242;adjP=0.0487
Renal cell carcinoma / Akt3; Pdgfb; Tgfb3; Pgf; Met; Pdgfa; Egln3; Pik3r1 / rawP=0.0250;adjP=0.0487
Gap junction / Pdgfb; Pdgfc; Pdgfa; Itpr1; Prkx; Plcb1; Lpar1; Plcb2; Src / rawP=0.0245;adjP=0.0487
Pancreatic secretion / Cd38; Atp2a3; Itpr1; Fxyd2; Plcb1; Plcb2; Pla2g2d; Atp1a3; Bst1; Atp1b3 / rawP=0.0252;adjP=0.0487

Supplemental Table 4: TGFR-dependent Colonic Macrophage Genes

Genes differentially regulated in colonic macrophages from CD11c-Cre-Tgfbr1fl/fl mice compared with Tgfbr1fl/fl mice selected from the 1004 genes significantly up- or down-regulated during the transition from monocyte to resident mɸ in the colon (Supplemental Table 1). t-test of MMS genes, PRaw ≤ 0.05, Fold Change ≥ 1.5

Downregulated in Cre+ macrophages / Upregulated in Cre– macrophages
Gene Symbol / Fold Change / Gene Symbol / Fold Change
Rnf180; Dnase1l3; Soga1; Sash1; Ptgs1; Pdia4; Pdgfa; Mylip; Slco3a1; Pdgfa; Ston2; Gna12; Gatm; Tgfbr1; Pdgfb; Rnf219; Mmp13; Slc7a4; Nbeal2; Enpp4; Fam214a; Cd9; Fry; Cebpa; Abcc3; Stk38l; 1110001A16Rik; 1810011H11Rik; Apoc1; Cxcl16; Gpr114; Hes1; Cd72; Tlr12; Mgat4a; Fam46c; Cd72 / ≥1.5 / Nrp2; Irak3; Cd4; Wwp1; Prkce; Pira11; Hbb-b2; 4930523C07Rik; Rgl1; Asap1; Scarb1; Pigz; Cdc42ep2; Asap1; Chn2; Vcam1; Rgl1; Sorbs3; Hpse / ≥1.5
Cmtm8; Cx3cr1; Fbxo32; Cx3cr1; Itgb5; Mylip; Cd33; Dgat2; Ecm1; Spata13; Arhgap22; Ntpcr; Cd276; Hic1; Kynu; Ccdc23; D8Ertd82e; Mvb12b; Spint1; Spint1; Kcnj10; Adam19; 2900026A02Rik; F11r; 8430419L09Rik; 8430419L09Rik; Rnf180; Ecm1; Hic1 / ≥2.0 / Ptgir; Irf7; Gpnmb; Nrp2; Ccl8; Hpse; Gdf15; Igf1; Csprs; Ccl24; Fpr1; Slc14a1; Pla2g2d; Emr4; Slc40a1; Mbnl3; Gm10522 / ≥2.0
Smad7; Mmp2; Vipr1; Sema4b; Cpd; Dtx4; Itgav; D8Ertd82e; Tnfsf13b; Zmynd15; Ccdc23; Pxdc1; Tgfbr1; Il22ra2; Il7r; Itgav; Pald1; Pmepa1; Pmepa1 / ≥3.0 / Spic; Igf1; Igf1; Igf1; Pla2g2d; Vcam1; Tdgf1 / ≥3.0
Zmynd15; Zfp691; Siglech; Tmem119 / ≥4.0 / C6 / ≥4.0
Tgfbr1 / ≥5.0 / Plcb1 / ≥12.0
Olfml3 / ≥7.0 / Mmp9; Plcb1 / ≥20.0
Olfml3; Capn3; Fam189a2 / ≥9.0
Ermap / ≥14.0
Capn3 / ≥17.0

Supplementary Table 5: List of Antibodies

Antibody / Clone / Source / Dilution
Mouse
Ly6G / 1A8 / Biolegend / 1/200
CD3ε / 145-2C11 / Biolegend / 1/200
CD19 / 6D5 / Biolegend / 1/200
CD45 / 30-F-11 / Biolegend / 1/200
CD11b / M1/70 / Biolegend / 1/200
CD11c / N418/HL3 / Biolegend/BD Biosciences / 1/200
MHCII (IA-IE) / M5/114.15.2 / Biolegend / 1/200
Ly6C / HK1.4 / eBioscience / 1/200
CD64 / X54-5/7.1 / Biolegend / 1/200
CD45.2 / 104 / Biolegend / 1/200
CD45.1 / A20 / Biolegend / 1/200
IL10 / JES5-16E3 / BD Biosciences / 1/200
TNF / MP6-XT2 / BD Biosciences / 1/200
CD9 / MZ3 / Biolegend / 1/200
CD63 / NVG-2 / Biolegend / 1/200
CD51 (v intregin) / RMV-7 / Biolegend / 1/200
CCR2 / 475301 / R&D Systems / 1/50
v5 / ALULA / Gift from Dr. Mark Travis / 1/200
CD274 / 10F.9G2 / Biolegend / 1/200
CD81 / Eat-2 / Biolegend / 1/200
7 integrin / M293 / BD Biosciences / 1/200
CD4 / RM4-4 / Biolegend / 1/200
MerTK / BAF591 / R&D Systems / 1/200
CD169 / 3D6.112 / Biolegend / 1/50
CD16/32 / 2.4G2 / Biolegend / 1/200
SiglecF / E50-2440 / BD Biosciences / 1/200
F4/80 / BM8 / Biolegend / 1/200
CD11a / M17/4 / Biolegend / 1/200
CD22 / OX-97 / Biolegend / 1/200
CD36 / HM36 / Biolegend / 1/200
CD38 / 90 / Biolegend / 1/200
CD206 / MR5D3 / AbDSerotec / 1/200
CLEC12A / 5D3 / Biolegend / 1/200
JAML / 4E10 / Biolegend / 1/50
LAIR-1 / 113 / eBiosciences / 1/200
Ly-108 / 13G3-19D / eBiosciences / 1/200
MGL2 / URA-1 / Biolegend / 1/200
PECAM-1 / MEC13.3 / Biolegend / 1/200
Tim4 / RMT4-54 / eBiosciences / 1/200
SA-PerCPCy5.5 / Biolegend / 1/200
SA-APC / eBiosciences / 1/200
FixableViability-eFluor506 or 780 / eBioscience / 1/1000
Live Dead 7-AAD / Biolegend / 1/20

Supplementary Table 6: List of Primers

Gene / Sense / Anti-sense
Cx3cr1 / TGT CCA CCT CCT TCC CTG AA / TCG CCC AAA TAA CAG GCC
Tgfbr1 / AGT GAT GGA TCC TCT TCA TTT / TTG CAC TTA TGC TGA TGG TCT
Il10 / GCT CTT ACT GAC TGG CAT GAG / CGC AGC TCT AGG AGC ATG TG