Table 1.
Top 10 marker genes used for the identification of specific cell clusters in scRNA‐seq data analysis.
| Cluster | Marker | Cluster | Marker | Cluster | Marker | Cluster | Marker |
|---|---|---|---|---|---|---|---|
| BECs | Fabp4 | Enteroendocrine cell 2 | Rbp2 | Macrophage 1 | S100a9 | Plasmacytoid dendritic cells | Bst2 |
| Ly6c1 | S100a6 | Cxcl2 | Siglech | ||||
| Igfbp7 | Lgals3 | Il1b | Ccl4 | ||||
| Plvap | Tm4sf20 | S100a8 | Rnase6 | ||||
| Ly6a | Serpinb6a | G0s2 | Mpeg1 | ||||
| Ptprb | Anxa2 | Srgn | Lsp1 | ||||
| Flt1 | Sprr2a3 | Tyrobp | Ly6c2 | ||||
| Pecam1 | Gsta1 | Cebpb | Cybb | ||||
| Cd36 | Fam162a | Cd14 | St8sia4 | ||||
| Epas1 | Pmp22 | Fcer1g | Ccr9 | ||||
| Bottom enterocytes | Reg3b | Erythroid cells | Hba‐a1 | Macrophage 2 | Lyz2 | Telocytes/Trophocytes | Dcn |
| Fabp1 | Hbb‐b1 | Ccl6 | Col3a1 | ||||
| Reg3g | Hba‐a2 | Ccl2 | Gsn | ||||
| Plac8 | Alas2 | Ccl9 | Col1a2 | ||||
| Sis | Ube2l6 | Mafb | Col1a1 | ||||
| Mgst1 | Snca | Ctsb | Mgp | ||||
| Maoa | Fech | Psap | Sfrp1 | ||||
| Arg2 | Cyb561d1 | Ctsc | Lum | ||||
| Aldh1a1 | Irgc1 | Lgmn | Bgn | ||||
| Gstm3 | Nudt15 | Ms4a6c | Serping1 | ||||
| CD4+ T cells | Emb | Fibroblasts | Apoe | Macrophage 3 | C1qa | Top Enterocytes | Apoa4 |
| Lat | Scn7a | C1qb | Ada | ||||
| Tcf7 | Sparc | C1qc | Apob | ||||
| Ms4a4b | Apod | Acp5 | Apoa1 | ||||
| Itgb7 | Fxyd1 | Apol7c | Clca4a | ||||
| Cd69 | Prnp | Il22ra2 | Apoc3 | ||||
| Lef1 | Cryab | Dnase1l3 | 2010109I03Rik | ||||
| Bcl11b | Plp1 | Pla2g2d | Selenop | ||||
| Cd27 | Chl1 | Batf3 | Nt5e | ||||
| Arl4c | Pmepa1 | Tctex1d2 | Dnpep | ||||
| CD8+ T cells | Ccl5 | Follicular B cells | Cd74 | Middle Enterocytes | Fabp2 | Tuft and M cells | Krt18 |
| Gzma | H2‐Ab1 | Guca2b | Cd24a | ||||
| Cd7 | Ly6d | Spink1 | Adh1 | ||||
| Cd3g | Vpreb3 | Anpep | Hck | ||||
| Rgs1 | Bank1 | Aldob | Sh2d6 | ||||
| Nkg7 | Cd83 | Clca4b | Lrmp | ||||
| Gzmb | Pou2f2 | Smim24 | Selenom | ||||
| AW112010 | Gpr183 | Slc5a1 | Tm4sf4 | ||||
| Cd8a | H2‐DMb2 | Leap2 | Dclk1 | ||||
| Cd3e | Fcmr | Guca2a | Avil | ||||
| Crypt cells | Krt19 | Goblet and Paneth cells | Zg16 | Myocytes/Pericytes | Acta2 | ||
| Dmbt1 | Tff3 | Tagln | |||||
| Gpx2 | Fcgbp | Myh11 | |||||
| Hmgb2 | Spink4 | Sparcl1 | |||||
| H2afz | Clca1 | Tpm1 | |||||
| Birc5 | Lgals2 | Tpm2 | |||||
| Ube2c | Agr2 | Cald1 | |||||
| Cks2 | Lypd8 | Myl9 | |||||
| Pclaf | Gm1123 | Rgs5 | |||||
| Ccdc34 | Ido1 | Flna | |||||
| Enteroendocrine cell 1 | Sct | LECs | Mmrn1 | Plasma cells | Jchain | ||
| Chgb | Ccl21a | Mzb1 | |||||
| Chga | Timp3 | Pou2af1 | |||||
| Neurod1 | Lyve1 | Nap1l1 | |||||
| Cpe | Cavin2 | Sec11c | |||||
| Krt7 | Reln | Dut | |||||
| Fxyd3 | Aqp1 | Eaf2 | |||||
| Reg4 | Flt4 | Mef2b | |||||
| Tph1 | Fgl2 | H2afx | |||||
| Pcsk1 | Tshz2 | Top2a |