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Table 1 Summary of gene expression analyses for combined clusters excluding cell cycle and nephron lineage clusters

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
C0 Stroma hFK 3 CKS2, LBH, CCBE1   SULT1E1, GPC3, MEG3, SERPINH1, ALDH1A2, TAGLN TAGLN, ALDH1A2, PDGFRA, ZEB2, ACTA2, ALX1, SNAI2, COL6A3
Org 2 NRK, STMN2  
C1 Stroma hFK 87 SERPINI1, COL1A1, S100A10, SFRP2, ANXA1, ASPN ECM organisation, signalling receptor binding DCN, COL1A1, LUM, IGF1, POSTN, SFRP2, COL1A2, OGN IGF1, SFRP2, COL1A1, DCN, LUM, COL1A2, COL3A1, POSTN
Org 5 RPL27A, PALLD, ACTA2, DKK1  
C2 Stroma hFK 11 REN, ID1, PDLIM1, ITGA8, ENG, CPM Endothelial and smooth muscle development DLK1, MGP, NDUFA4L2, GATA3, APOE, PDGFRB, MEF2C MGP, GATA3, NDUFA4L2, MEF2C, ACTA2, PDGFRB, PDLIM1
Org 2 SSBP4, FTL  
C3 Stroma hFK 23 ACTA2, NR2F1, ANGPT1, ROBO2 No significant results MAB21L2, CXCL14, PRRX1, ZFHX4, MAB21L1, CD24, COL9A2 ZFHX4, CTSK, HNRNPA1, DNM3OS, SOX4, LIMA1, TBX3
Org 12 VIM, VAMP2, SNHG8, DKK1 Mitochondrial ribosome binding
C4 Endothelium hFK 45 FN1, RBP5, PLPP3, CCL21, LGALS1, CXCL1, CXCL2, CXCL8, ICAM1 Signalling receptor binding, chemokine activity GNG11, EGFL7, CLDN5, ESAM, PVLAP, CD34, CAV1, ARHGAP29, APLN GNG11, EGFL7, CLDN5, ESAM, PVLAP, S100A16, ARHGAP29, APLNR, CAV1, CD34, KDR, TIE1
Org 44 APLN, PECAM1, MMP1, CAV1, CXCR4, HEY1 Angiogenesis, vascular development
C9 Stroma hFK 67 COL1A1, PLPP3, ITM2B, IGF1, SPON2 Cell adhesion, ECM organisation COL2A1, COL9A3, CNMD, MIA, COL9A2, COL9A1, FIBIN COL9A3, DCN, LUM, FIBIN, COL1A2, OGN, IGFBP6, COL1A1, SOX9, SFRP2, MGP
Org 41 CNMD, PEG10, COL9A1, COL9A3, GNG5, COL11A1 ECM organisation, cartilage dev.
C11 Glia hFK 203 S100B, PLP1, MPZ, PMP22, ARHGAP15 Axon development AP1S2, TTHY1, FABP7, SOX2, MSX1, PCSK1N S100B, GPM6B, TTYH1, PLP1, SOX2, NKAIN3, PMP22, CNP, VIM
Org 136 AP1S2, FABP7, ZFP36L1, MSX1 ATP synthesis, cell respiration
C12 Immune hFK 88 HLA-DPB1, HLA-DPA1, HLA-DRB1, CXCR4, CD83 Response to IFN gamma, antigen binding HLA-DRA, CD74, SRGN, S100A9, TYROBP, S100A8, HLA-DPB1, LYZ SRGN, LYZ, S100A9, TYROBP, S100A8, FCER1G, SPP1, FTL, CD74
Org 24 PRTN3, MPO, CTSG, AZU1 Immune response, defence response
C13 Blood hFK 24 HBM, AHSP, ALAS2, HEMGN, SLC25A37 Erythrocyte development, oxygen transport HBG1, HBB, HBA2, HBA1, HMB, AHSP, ALAS2, SCNA, GNG11, HEMGN CYPC, SLC25A39, SLC25A37, GPX1, HEY1, COPZ1, PRDX2, ACTB, SELENBP1, PFN1
Org 168 FSCN1, EGFL7, FKBP1A, EIF4G2, GNG5, TPM4, BAX Viral process, translation initiation
C14 Neural hFK N/A    HES6, CRABP1, TUBB2B, STMN2, TAGLN3, SSTR2 N/A
Org N/A   
  1. Abbreviations: DE differentially expressed (adjusted p value < 0.05, absolute log fold change greater than 0.8), ECM extracellular matrix. Full lists available in Additional files and on website [32]