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Table 2 Summary of gene expression analyses for combined nephron clusters excluding stromal cluster CN6

From: Single-cell analysis reveals congruence between kidney organoids and human fetal kidney

Cluster and sample origin DE Top enriched genes GO summary for ≥ 10 DE genes Top cluster markers Top conserved markers
CN0 Pod hFK 79 TUB1A1, NR2F1, SOX4, LGALS1, NUSAP1, LYPD1 Central nervous system development S100A6, TCF21, PODXL, TPPP3, SBSPON, MMP5, CPXM1, DUSP23, THSD7A, MME TCF21, MME, PODXL, THSD7A, TPPP3, SBSPON, MAFB, ENPEP, ROBO2, NPHS2
Org 175 VAMP8, ANXA1, AIF1, S100A4, TGFBR3, WT1 ATP synthesis, oxidative phosphorylation
CN1 Diff. NP hFK 37 CCND1, PCNA, CXCR4, TUBA1A, TBUA1B, STMN1 mRNA splicing LYPD1, PAX8, HIST1H4C, PCLAF, CDH6, DAPL1, CCND1, RBP1, HMGB2 LYPD1, PAX8, HIST1H4C, PCLAF, DAPL1, PCP4, HEY1, CDH6, RBP1, PAX2
Org 4 FTL, GNAS, BNIP, ATOX1  
CN2 NP hFK 24 TMEM100, ITM2C, MEOX1, EPCAM, ROBO2, DAPL1 Amyloid precursor biosynthesis ACTC1, NNAT, MYLPF, MYL1, TMEM100, TPM2, CRABP2, TUB1A1 NNAT, CRABP2, TUB1A1, IGF2, SIX1, TMEM100, CITED1, SOX4, MEOX1, MEIS2
Org 25 ACT1C1, MYLPF, TPM2, PITX2, MYOG, MYOD Muscle filament sliding
CN3 Pod. Pre. hFK 37 CCND1, OLFM3, CXCL1, HNRNPR, STMN1 No significant BP terms CTGF, GPX3, TSPAN8, PAPPA, PAPPA, ITIH5, SERINC5, HES4, NPHS2, NPHS1, MAFB, PTPRO CTGF, OLFM3, BCAM, NPHS1, ARHGAP29, CLDN1, LEPROT, TMP1, STON2, CLDN5, MAFB
Org 78 GPX3, ANXA1, S100A4, AIF1, PTPRO, SYNPO, VEGFA, WT1 Epithelial cell diff. involved in kidney development
CN4 Distal hFK 26 PTGR1, MAL, LIMCH1, ELF3, ALDH1A1, PAPPA2 Epithelium development HBG2, ATF3, LIMCH1, MAL, WFDC2, BTG2, HES1, KLF6, MECOM, ELF3, TUBB2B, GATA3 WFDC2, EMX2, LIMCH1, MAL, TUBB2B, SAT1, MECOM, HMGA1, HES1, GATA3, ATP1B1, GNG11
Org 11 LHX1, BNIP3, FTL, CKB, BASP1, CITED2, HNRNPAB Kidney morphogenesis
CN5 Proximal hFK 34 CCND1, CA2, VCAN, ELF3, DCDC2, FLRT3 No significant BP terms IGFBP7, CD24, PCP4, PCSK1N, FXYD2, EMX2, MPC2, APOE, CLU, CFAP126, FTL, ATP1B1 IGFBP7, MPC2, SMIM24, FLRT3, EMX2, FXYD2, GNG11, TSPAN12, CLU, PCP4, ATP1B1, PDZK1
Org 14 PCSK1N, CITED2, BNIP3, S100A13, MLLT1, PRDX5, VAMP8, LHX1 Ureteric bud morphogenesis, pronephros development
CN7 hFK Pod hFK     CXCL12, TNNI1, TNNT2, MME, MYL9, MRGPRF, TPPP3, ANXA2, COL4A4, ADM, PTPRO, MSMO1 N/A
Org    
  1. Abbreviations: DE differentially expressed (adjusted p value < 0.05, absolute log fold change greater than 0.8), hFK human fetal kidney, Org organoid. GO summary reporting top significant Gene Ontology (GO) Biological process (BP) results when fetal kidney or organoid DE gene lists were greater than or equal to ten genes. Full lists of cluster markers, conserved and differentially expressed genes and corresponding GO analyses available in Additional files or on website [32]