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

Reference

Model usage

Holloway et al. [21, 22]

Train

Hochane et al. [23, 24]

Train

Tran et al. [25, 26]

Train

Test

Lindstrom et al. [27, 28]

Test

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

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