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Table 1 Summary of datasets used in this manuscript, including human fetal kidney and human kidney organoids

From: DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets

Human fetal kidney
Reference Age (post coitum) Sample details Model usage
Holloway et al. [21, 22] 16 weeks Wedge biopsy including both medulla and cortex, 1 day 96 male and 1 day 108 female samples Train
Hochane et al. [23, 24] 11, 13, 16 and 18 weeks Week 9, 11, 13, 16 and 18 kidney pieces Train
Tran et al. [25, 26] 17 weeks Regions dissected from both inner and outer cortex Train
15 weeks Regions dissected from both inner and outer cortex Test
Lindstrom et al. [27, 28] 16 weeks MARIS dissociation used to isolate cortical regions Test
Kidney organoids
Reference & repository Age (days) Protocol Sample information ID Initial classification
Wu et al. [12, 29] 26 Takasato 4 batches of iPS and 2 batches of ES-derived organoids Wu_T Clustering & DE genes, Integration with self-generated adult snRNA dataset,
Lindstrom [27] trained random forest classifier
26 Morizane 3 batches of iPS and 1 batch of ES-derived organoids Wu_M
34 Takasato iPS-derived organoid extended culture Wu_TO
7, 12, 19, 26 Takasato Time course of iPS-derived organoids Wu_TC
26 Takasato (modified) 2 batches of iPS-derived organoids with BDNF inhibition Wu_TB
Czerniecki et al. [30, 31] 21 Freedman iPS- and ES-derived organoids, modified protocol for high throughput sequencing Cz_F Clustering & DE genes, Menon [32]
21 Freedman (modified) iPS- and ES-derived organoids, modified protocol for high throughput sequencing, VEGF addition Cz_VEGF_F
Howden et al. [13, 33] 18, 25 Takasato iPS-derived organoids using E6 base media How_T Clustering & DE genes
Phipson et al. [20, 34], Combes et al. [15] 25 Takasato iPS-derived organoids generated in two batches. Same dataset in both publications Phip_T Clustering & DE genes; Integration with Lindstrom [27]
Harder et al. [35, 36] 19,21 Freedman ES-derived organoids, 6 datasets generated from the all organoids in a well, 3 separate batches Har_F Clustering & DE genes, integration and trajectory analysis with Menon [32]
20 Freedman A single ES-derived organoid isolated from a full well Har_F_SO
Subramanian et al. [14, 37] 7, 15, 29, 32 Takasato iPS-derived organoids with 3 pooled replicates per time using iPS cell line designated “ThF” Sub_T_L1 Clustering & DE genes, organoid trained random forest classifier, integration with Young [38], Lindstom [27] and self-generated kidney tissue
7, 15, 29 Takasato iPS-derived organoids with 3 pooled replicates per time using iPS cell line designated “AS” Sub_T_L2
Kumar et al. [19, 39] 25 Kumar (Takasato modified) iPS-derived micro-organoid in suspension culture Ku Integration with organoid [15, 20] with clustering & DE genes
Low et al. [40, 41] 10, 12, 14 Low (novel) Use three distinct phases of Wnt signalling, “defining”, “priming” and “patterning” the differentiating cells towards kidney organoid Low Clustering & DE genes
Tran et al. [25, 26] 16, 28 Morizane ES-derived organoids Tran_M Clustering & DE genes individually & after integrating with self-generated kidney tissue
Lawlor, Vanslambrouck, Higgins et al. [42, 43] 25 Takasato iPS-derived organoids generated by bioprinting. Organoids were compared with three different biophysical properties. LVH_T Clustering & DE genes compared to Hochane [24] trained machine learning model using scPred
Uchimura et al. [44, 45] 26 Takasato (modified) iPS-derived organoids cultured following the Takasato protocol to day 7, before following Uchimura protocol to day 26 Uch_T Clustering & DE genes, comparison to Wu [12] using pairwise Pearson correlation
26 Uchimura (novel) iPS-derived organoids generated by combining AIM and PIM differentiations in a 1:3 ratio at day 7 before culturing in modified maturation media novel to this protocol Uch_U
Wilson et al. (this publication) 25 Takasato (modified) iPS-derived organoids generated in the same batch as Howden et al. [13] with RA treatment at day 12 Wil_TM Direct comparison to existing organoids using DevKidCC
Ureteric bud organoids
Howden, Wilson et al. [46, 47] NA Howden Takasato iPS derived organoids dissociated and GATA3+EPCAM+ cells isolated. These cells cultured in ureteric epithelium promoting conditions. HW_iUB Seurat Label Transfer using reanalysed Holloway
Mae et al. [48, 49] NA Mae Induced Ureteric Bud cultures Mae_iUB Clustering & DE genes