|
Antibodies and Probes
|
SOURCE
|
IDENTIFIER
|
| anti-Ap-2-α |
Cell Signaling |
3215S |
| anti-Cdh1 |
BD Transduction laboratories |
610182 |
| anti-Cdh6 |
R&D |
AF2715 |
| anti-Cldn5 |
Novus Biologicals |
NB120–15107 |
| anti-Emx2 |
R&D |
AF6470 |
| anti-Erbb4 |
R&D |
MAB1131 |
| anti-Foxc2 |
R&D |
AF6989 |
| anti-Hnf1b |
Santa Cruz |
sc-22840 |
| anti-Hnf4a |
R&D |
MAB4605 |
| anti-Irx1 |
SIGMA |
HPA043160 |
| anti-Jagged1 |
R&D |
AF599 |
| anti-Krt8 |
DSHB |
TROMA-1 |
| anti-Lef1 |
Cell Signaling |
2230 |
| anti-Lhx1 |
Santa Cruz |
sc-19341 |
| anti-Mafb |
R&D |
MAB3810 |
| anti-Mafb |
Santa Cruz |
sc-10022 |
| anti-Mecom |
R&D |
MAB75061 |
| anti-Pappa2 |
R&D |
AF1668 |
| anti-Pax2 |
Biolegend |
901001 |
| anti-Pax8 |
Abcam |
ab189249 |
| anti-Podxl |
R&D |
AF1658 |
| anti-Pou3f3 |
Thermo Scientific |
PA5–64311 |
| anti-Pou3f3 |
Novus Biologicals |
NBP1–49872 |
| anti-Sall1 |
R&D |
PP-K9814–00 |
| anti-Six2 |
Mybiosource |
MBS610128 |
| anti-Six2 |
ProteinTech |
11562–1-AP |
| anti-Sox9 |
Abcam |
ab185230 |
| anti-Tfcp2l1 |
Novus Biologicals |
AF5726 |
| anti-Tfap2a |
Cell Signaling |
3215 |
| anti-Tfap2b |
Cell Signaling |
2509S |
| anti-Wt1 |
Abcam |
ab89901 |
| RNA-Scope SLC39A8
|
ACD |
556831 |
| RNA-Scope TMEM72
|
ACD |
556851-C2 |
| RNA-Scope COL4A4
|
ACD |
557261-C3 |
| RNA-Scope LAMP5
|
ACD |
487691-C3 |
| RNA-Scope HNF4A
|
ACD |
442921-C2 |
| RNA-Scope EFNB2
|
ACD |
430651 |
|
|
|
|
Deposited data
|
GEO accession number
|
Reference
|
| Human week 14 scRNA-seq data |
GSE139280 |
(this study) |
| Zonal Human week 17 scRNA-seq data |
GSE127344 |
(Tran et al., 2019) |
| Adult mouse nephron scRNA-seq |
GSE129798 |
(Ransick et al., 2019) |
|
|
|
|
Experimental models: Organisms/strains
|
|
|
| Swiss Webster mice |
Lab stock |
|
|
|
|
|
Software and algorithms
|
URL
|
DOI/Reference
|
| ANTs |
https://github.com/ANTsX/ANTs
|
10.5281/zenodo.5138159
|
| Woolz |
https://github.com/ma-tech/Woolz
|
10.5281/zenodo.5138133
|
| Registration pipeline |
https://github.com/ma-tech/RenalObjectRegistrationPipeline
|
10.5281/zenodo.5138175
|
| Amira versions 6.1.1, 6.2, and 6.3 |
Themofisher |
|
| CellRanger version 2.1 |
10xgenomix |
|
| Code for 3D protein patterns & single-cell + spatial data integration |
https://github.com/flatironinstitute/fetal_kidney_clusters
|
10.5281/zenodo.5138196
|
| Code for Bayesian integration |
https://functionlab.github.io/sleipnir-docs/index.html
|
(Huttenhower et al., 2008) |
| Seurat v2, 3, 4 |
https://satijalab.org/seurat/
|
(Butler et al., 2018; Stuart et al., 2019) |
|
|
|
|
Additional resources
|
URL
|
Reference
|
| Human Nephrogenesis Atlas |
https://sckidney.flatironinstitute.org
|
this study |
