Table 4. Top 20 differentially expressed genes per cluster.

The FindAllMarkers function was used to identify the top differentially expressed genes for each cluster across all timepoints. Genes were sorted from highest to lowest average log2 fold change (avg_log2FC) values within each cluster. Genes of interest shown in red. Full dataset found in Table 4—source data 1.

M	HEP1	HEP0	HEP4	HEP3	NC-C	CN-M2	HEP5	CN-M1	CN	EC2	NC-P	HEP2	EC1	rep HEP	OG
0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15
Mmp2	Spink1	Mup11	Acot3	Mup21	Ewsr1	Col11a1	Gm31583	Ptgs2	F13a1	Hbb-bt	Hcar2	Elovl3	Derl3	Ly6d	Ccl8
Aebp1	Gstm3	Mup17	Cyp4a14	Elovl3	Parp10	Ptprn	Mpo	Il11	Cxcl3	Hba-a1	Cxcl3	Cyp4a12b	3930402G23Rik	Moxd1	Gm32468
Olfml3	Ifi27l2b	Cyp2b13	Cyp2c69	Serpina1e	Fth1	Ccl11	Gdf10	Cxcl10	Pf4	Hba-a2	Ptges	Hsd3b5	Hyou1	BC049987	Kdelr3
Cd74	Klk1b4	Mup12	Sult2a1	Cib3	Ptprc	Prnd	Cd207	Cxcl9	Mmp9	Hbb-bs	Tnf	Gm32468	Sult3a1	Esco2	Hbb-bt
Pacs2	Vnn3	Mup16	Cyp2a4	Sds	Csf3r	Cthrc1	Gck	Il6	Ptges	mt-Atp8	Ccl4	Lhpp	Sdf2l1	Gsta1	Cyp1b1
Ngp	Cib3	Mup7	Cyp4a10	Mfsd2a	Pacs2	Gpnmb	Cyp8b1	Serpine1	Cstdc4	mt-Nd4l	Cxcl2	Cyp4a12a	Apcs	Cdkn3	Lgals1
Ewsr1	Cdh1	Mup1	Sult2a2	Acmsd	Lyn	Actg2	Abcd2	Hspa1a	Gpr84	Malat1	Il1f9	Fitm1	Pdia4	Chrna4	Vwf
Clu	Frzb	Mup3	Fmo3	Slc22a7	Osbpl9	Fbln2	1700001C19Rik	Adm	Itgam	mt-Nd3	Fth1	Oat	Dnajb9	Nat8	Cthrc1
Cdk11b	Spon2	Cyp2b9	Slc16a5	Etnppl	Hectd1	Col12a1	Defb1	Gm15056	Fpr2	mt-Nd5	Ccl3	Slc1a2	A1bg	Nat8f5	Cpe
Parp8	Snta1	Cyp7b1	Cyp2b9	Slc10a2	Iqgap1	Sulf1	Prox1os	Nos2	Adam8	mt-Nd2	Slfn4	Cyp2a5	Prg4	Mup1	Pcdh17
Nisch	Wfdc2	Mup20	A1bg	Selenbp2	Clk1	Mmp13	Socs2	Gbp5	Lyz2	mt-Co2	Asprv1	Tuba8	Gm26917	Thrsp	Rasl11a
Cpxm1	Gstm2	Gm13775	Cyp2c40	Mmd2	Lilr4b	Sfrp1	Bik	Olr1	Clec4d	Elane	Slc7a11	Cyp2c55	Mt2	Gm32468	Ccdc80
Poglut1	Spic	mt-Atp8	Slc22a27	G6pc	Thrap3	Fkbp10	Afmid	Rnd1	Cav1	Gm26917	Acod1	Rhbg	Cyp17a1	Cdca3	Mrc2
Col6a2	Tmem268	Mup9	Cyp2c37	Arl4d	Stip1	Lox	Rad51b	Retnlg	Mmp8	mt-Atp6	Slpi	Slc13a3	Creld2	Hebp2	Hbb-bs
Loxl1	Tstd1	Serpina3m	Cyp2c38	Kcnk5	Fbxl5	Acta2	1810059H22Rik	Il1a	Il1f9	mt-Nd1	Ccrl2	Cyp7a1	Vnn1	Ect2	Ccbe1
Gpx3	Prelp	Itih4	Acot1	Lpin1	Zfp207	Col15a1	Tmem25	F3	Fpr1	mt-Nd4	Il1rn	Glul	Hist1h4h	Pbk	mt-Nd1
Col1a1	Slc39a4	Slco1a1	Etnppl	Tat	Klf2	Nbl1	Angptl6	Cxcl2	Capg	Gm29966	Slc25a37	Slc1a4	Rcan2	Cdc20	Plxdc2
Igha	Mki67	Cyp2b10	Gstt3	Upp2	Hck	Col5a2	Fam89a	Procr	Stfa2l1	mt-Co3	Mmp12	Rdh16	Hspa5	Gpam	Nat8f5
Ikbkb	Cdk1	Car3	Gm13775	Pck1	Rhob	Col5a1	Mug1	AA467197	Pqlc3	Gm42418	Clec4e	Serpina7	mt-Atp6	Nek2	Chrna4
Rpl4	Mcm5	Fbxo31	Ptgds	Fam47e	Lilrb4a	Tnc	Ccl27a	Plaur	Pdpn	mt-Co1	Il1b	Cyp1a2	mt-Co2	Aurka	Snhg18