. 2024 Nov 16;25:412. doi: 10.1186/s12882-024-03853-y

Table 3.

The scale and resolution of single-cell transcriptomics studies in nephrology

Article information	cell number analyzed	Total number of gene	Cell number of DEG^a	Public databases
Park et al. (2018) [45]	57,979	\	PC: 870 Trans: 110 IC: 1,729	NCBI GEO (GSE107585)
Fu et al. (2019) [46]	644	2,226,308	EC: 369 MC: 144 Pod: 66	NCBI GEO (GSE127235)
Dumas et al. (2020) [47]	40,662	15,977	gRECs: 15,419 cRECs: 11,762 mRECs: 13,481	ArrayExpress (E-MTAB-8145)
Chung et al. (2020) [48]	75,000	1,070	Pod: 1,930 EC: 1,858 MC: 1,197	NCBI GEO (GSE146912)
Braun et al. (2021) [49]	164,722	6,260	Immune Tumor	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8138872/
Krishna et al. (2021) [50]	167,283	16,323	Immune Tumor	https://linkinghub.elsevier.com/retrieve/pii/S1535610821001653
Obradovic et al. (2021) [51]	200,000	30,727	Immune Tumor	10.17632/nc9bc8dn4m.1
He et al. (2021) [52]	4,332	973(Pod: 424, GECs: 196, MCs: 353)	Pod: 224 GECs: 241 MCs: 17 PECs: 44	NCBI GEO (GSE160048); EGA (EGAD00001006861); https://ega-archive.org/access/dataaccess; https://patrakkalab.se/kidney
Pickering et al. (2021) [53]	34,182	3,000	NK and CD8 + T cell	NCBI GEO (GSE168598, PRJNA745955); ImmPort (SDY1600).
Sheng et al. (2021) [54]	60,661	19,315	PT: 251 Th17: 254 NK: 237 EdnoG: 229	NCBI GEO (GSE173343, GSE115098, GSE172008); http://susztaklab.com/HumanKidneysnATAC/; https://susztaklab.com/VisCello/
Li et al. (2022) [55]	309,666	\	PT: 76,400 TAL: 25,600 DCT: 10,900 CNT: 42,600	http://humphreyslab.com/SingleCell/; NCBI GEO (GSE190887, GSE206084)
Wu et al. (2022) [56]	946,660	8,248	PCs TAL: PECs PT ECs	NCBI GEO (GSE184652, GSE199437); http://humphreyslab.com/SingleCell/
Lu et al. (2022) [57]	\	31,077	10 cell types (tubular cells, endothelium, …)	https://www.frontiersin.org/articles/10.3389/fcell.2022.798316 https://doi.org/10.3389/fcell.2022.798316
Li et al. (2022) [58]	270,000	\	Immune PT Fibroblasts	10.17632/g67bkbnhhg.1 https://www.sanger.ac.uk/project/microenvironment-of-kidney-cancer
Kong et al. (2022) [59]	39,285	53,664,695	T cells B cells	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190329
Rashmi et al. (2022) [60]	50,275	20,150	Immune: 21,038 PT: 11,887 Endo: 13,294	www.kpmp.org
Lake et al. (2023) [61]	400,000	\	PT TAL Immune	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA671343
Wen et al. (2023) [63]	81,139	\	EC, immune, stromal, Endo	\
Liu et al. (2023) [67]	70,944	740	PT Mesan Pod	NCBI GEO (GSE218563, GSE218086, GSE218413)
Tsai et al. (2023) [69]	6,775	\	Tubular: 5938 Lymphoid: 323 Myeloid: 130 Pod: 19 MC: 21 EC: 202	\
Balzer et al. (2023) [70]	4,821	4,265	PT	NCBI GEO (GSE209821) http://www.susztaklab.com/ZSF1_sGC_snRNA/
Aidan et al. (2024) [64]	31,203	>20	Immune: 3,117 PT: 1,656 GEC: 9,28	NCBI GEO (GSE189536)
Lu et al. (2024) [65]	23,980	\	Immune	National Genomics Data Center (HRA004752, HRA005498)

^a The numbers listed in this column represent the number of cells expressing the gene. These cell types are representative part of a broader dataset and not an exhaustive representation of all cell types present in our analysis because of space limitations in table

Abbreviations: DEG differentially expressed genes, PT proximal tubule, IC intercalated cell, Endo endothelial cells, PCs principal cells, TAL thick ascending limb, PECs parietal epithelial cells, ECs endothelial cells, GEO Gene Expression Omnibus, MC mesangial cells, Pod podocytes, RECs renal endothelial cells, GECs glomerular endothelial cells, EndoG glomerular endothelial cells, Th17 T helper 17 cells, NK natural killer cells