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 |