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 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
CN0 Pod	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
CN1 Diff. NP	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
CN2 NP	Org	25	ACT1C1, MYLPF, TPM2, PITX2, MYOG, MYOD	Muscle filament sliding	ACTC1, NNAT, MYLPF, MYL1, TMEM100, TPM2, CRABP2, TUB1A1
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
CN3 Pod. Pre.	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
CN4 Distal	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
CN5 Proximal	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
CN7 hFK Pod	Org					N/A

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]

Back to article page

ISSN: 1756-994X

Contact us

Submission enquiries: editorial@genomemedicine.com
General enquiries: info@biomedcentral.com

Genome Medicine

Contact us