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

Combes, Alexander N.; Zappia, Luke; Er, Pei Xuan; Oshlack, Alicia; Little, Melissa H.

doi:10.1186/s13073-019-0615-0

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
C0 Stroma	Org	2	NRK, STMN2		SULT1E1, GPC3, MEG3, SERPINH1, ALDH1A2, TAGLN	TAGLN, ALDH1A2, PDGFRA, ZEB2, ACTA2, ALX1, SNAI2, COL6A3
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
C1 Stroma	Org	5	RPL27A, PALLD, ACTA2, DKK1		DCN, COL1A1, LUM, IGF1, POSTN, SFRP2, COL1A2, OGN	IGF1, SFRP2, COL1A1, DCN, LUM, COL1A2, COL3A1, POSTN
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
C2 Stroma	Org	2	SSBP4, FTL		DLK1, MGP, NDUFA4L2, GATA3, APOE, PDGFRB, MEF2C	MGP, GATA3, NDUFA4L2, MEF2C, ACTA2, PDGFRB, PDLIM1
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
C3 Stroma	Org	12	VIM, VAMP2, SNHG8, DKK1	Mitochondrial ribosome binding	MAB21L2, CXCL14, PRRX1, ZFHX4, MAB21L1, CD24, COL9A2	ZFHX4, CTSK, HNRNPA1, DNM3OS, SOX4, LIMA1, TBX3
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
C4 Endothelium	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
C9 Stroma	Org	41	CNMD, PEG10, COL9A1, COL9A3, GNG5, COL11A1	ECM organisation, cartilage dev.	COL2A1, COL9A3, CNMD, MIA, COL9A2, COL9A1, FIBIN
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
C11 Glia	Org	136	AP1S2, FABP7, ZFP36L1, MSX1	ATP synthesis, cell respiration	AP1S2, TTHY1, FABP7, SOX2, MSX1, PCSK1N	S100B, GPM6B, TTYH1, PLP1, SOX2, NKAIN3, PMP22, CNP, VIM
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
C12 Immune	Org	24	PRTN3, MPO, CTSG, AZU1	Immune response, defence response	HLA-DRA, CD74, SRGN, S100A9, TYROBP, S100A8, HLA-DPB1, LYZ	SRGN, LYZ, S100A9, TYROBP, S100A8, FCER1G, SPP1, FTL, CD74
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
C13 Blood	Org	168	FSCN1, EGFL7, FKBP1A, EIF4G2, GNG5, TPM4, BAX	Viral process, translation initiation	HBG1, HBB, HBA2, HBA1, HMB, AHSP, ALAS2, SCNA, GNG11, HEMGN
C14 Neural	hFK	N/A			HES6, CRABP1, TUBB2B, STMN2, TAGLN3, SSTR2	N/A
C14 Neural	Org	N/A			HES6, CRABP1, TUBB2B, STMN2, TAGLN3, SSTR2	N/A

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]

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ISSN: 1756-994X

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