Table 1.

Selected transcriptional profiling studies after kidney injury

Study	Species	Source	Type of data	Cell-type specification	Transcription factor analysis
Liu et al. (49)	Mouse	Whole kidney	Microarray	TRAP for Six2 (nephron), Foxd1 (interstitial), Cdh5 (endothelial), and Lyz2 (myeloid)	Ingenuity canonical pathway analysis
Chang-Panesso et al., 2019 (47)	Mouse	Whole kidney	RNA-Seq	TRAP for Kim1	Transcription factor expression
Kirita et al., 2020 (21)	Mouse	Whole kidney	snRNA-Seq	Clustering with annotation	SCENIC (50)
Legouis et al., 2020 (98)	Mouse	Whole kidney	snRNA-Seq	Clustering, Six2 enriched	PROGENy (99)
Rudman-Melnick et al., 2020 (100)	Mouse	Whole kidney	scRNA-Seq	Clustering with annotation	Transcription factor expression
Gerhardt et al., 2021 (83)	Mouse	Whole kidney	snRNA-Seq	Clustering, Krt20 and Six2 enriched	SCENIC (50)
Ide et al., 2021 (23)	Mouse	Whole kidney	scRNA-Seq	Clustering with annotation	Not specifically assessed
Balzer et al., 2022 (22)	Mouse	Whole kidney	scRNA-Seq	Clustering with annotation	SCENIC (50)
Ide et al., 2022 (97)	Mouse	Whole kidney	scRNA-Seq	Clustering with annotation	SCENIC (50)
Li et al., 2022 (101)	Mouse	Whole kidney	snRNA-Seq	Clustering with annotation	DoRothEA (102, 103)
Gerhardt et al., 2023 (20)	Mouse	Whole kidney	snRNA-Seq, snATAC-Seq	Clustering, Ki67 enriched	chromVAR (51)
Lake et al., 2023 (6)	Human	Research biopsies	sc/snRNA-Seq, SNARE-Seq, spatial transcriptomics	Clustering with annotation	chromVAR (51)
Li et al., 2024 (104)	Human	Kidney regions	snRNA-Seq, snATAC-Seq (SHARE-Seq)	Clustering with annotation	PROGENy (99), chromVAR (51)

Abbreviation: TRAP, translating ribosome affinity purification.