KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-Aqp1 | Abcam | Cat# ab168387; RRID: AB_2810992 |
| Mouse monoclonal anti-Aqp2 | Santa Cruz | Cat# sc-515770; RRID: AB_2810957 |
| Rabbit monoclonal anti-Atp6v1b1 | Abcam | Cat# ab192612; RRID: AB_2810993 |
| Mouse monoclonal anti-Calb1 | Sigma | Cat# C9848; RRID: AB_476894 |
| Rabbit polyclonal anti-Ckb | LSBio | Cat# LS-C662557; RRID: AB_2810994 |
| Chicken polyclonal anti-GFP | Chemicon | Cat# AB16901; AB_90890 |
| Rabbit polyclonal anti-Hoxd10 | Abcam | Cat# ab76897; RRID: AB_2041677 |
| Goat polyclonal anti-Jag1 | R&D Systems | Cat# AF599; RRID: AB_2128257 |
| Rabbit polyclonal anti-Slc26a4 | Sigma | Cat# SAB2104723; RRID: AB_10669168 |
| Rabbit anti-Slc4a1 | Alpha Diagnostics | Cat# AE11-A; RRID: AB_1609266 |
| Rabbit polyclonal anti-Slc5a2 | Abcam | Cat# ab85626; RRID: AB_10674183 |
| Rabbit polyclonal anti-Rhbg | Novus | Cat# NBP2–33527; RRID: AB_2810996 |
| Goat polyclonal anti-TFCP2L1 | R&D Systems | Cat# AF5726; RRID: AB_2202564 |
| Fluorescent In Situ hybridization probes | ||
| Ache | Advanced Cell Diagnostics | Cat# 490021-C2 |
| Acsm3 | Advanced Cell Diagnostics | Cat# 533841-C3 |
| Cyp2e1 | Advanced Cell Diagnostics | Cat# 402781 |
| Cyp2e1 | Advanced Cell Diagnostics | Cat# 402781-C2 |
| Cyp4a14 | Advanced Cell Diagnostics | Cat# 566301-C3 |
| Cyp7b1 | Advanced Cell Diagnostics | Cat# 471001 |
| Fst | Advanced Cell Diagnostics | Cat# 454331 |
| Gdf15 | Advanced Cell Diagnostics | Cat# 442941 |
| Prlr | Advanced Cell Diagnostics | Cat# 430791-C2 |
| Sh2d4b | Advanced Cell Diagnostics | Cat# 564941 |
| Slc14a2 | Advanced Cell Diagnostics | Cat# 476721 |
| Slc22a7 | Advanced Cell Diagnostics | Cat# 557271-C3 |
| Slc2a9 | Advanced Cell Diagnostics | Cat# 564911-C3 |
| Slc34a1 | Advanced Cell Diagnostics | Cat# 428141-C2 |
| Slc39a8 | Advanced Cell Diagnostics | Cat# 425991 |
| Slc7a12 | Advanced Cell Diagnostics | Cat# 556841 |
| Slc7a13 | Advanced Cell Diagnostics | Cat# 556861-C2 |
| Sptssb | Advanced Cell Diagnostics | Cat# 564891-C3 |
| Biological Samples | ||
| Healthy adult mouse kidney | C57BL/6J mice | Jackson Lab Stock No: 000664 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| B. licheniformis protease | CreativeEnzymes | Cat# NATE-0633 |
| DNase I | Worthington | Cat# LS002058 |
| Collagenase, type 2 | Worthington | Cat# LS00417 |
| Fetal Bovine Serum | ThermoFisher Sci. | Cat# 12662029 |
| DPBS | VWR | Cat# 16777–259 |
| Tamoxifen | Sigma Aldrich | Cat# H7904 |
| Formaldehyde 16% in aqueous solution, EM Grade | EMS thru VWR | Cat# 15711 |
| SeaBlock | ThermoFisher Sci. | Cat# 37527 |
| MatTek glass bottom dishes | MatTek Corp. | Cat# P35G-0–20-C |
| DAPI | ThermoFisher Sci. | Cat# D1306 |
| DRAQ5 | ThermoFisher Sci. | Cat# 62254 |
| Hoechst 33342 | ThermoFisher Sci. | Cat# H3570 |
| 40um Cell Strainer (coarse) | Falcon, CorningLife science | Cat# 352340 |
| 40um Cell Strainer (fine) | VWR | Cat# 21008–949 |
| AutoMACs Running Buffer | Miltenyi Biotec | Cat# |
| Tissue-Tek® O.C.T. Compound | VWR | Cat# 25608–930 |
| Critical Commercial Assays | ||
| Chromium Single Cell 3’ Library & Gel Bead Kit v2 | 10X Genomics | Cat# 120237 |
| Chromium Single Cell A Chip Kit | 10X Genomics | Cat# 120236 |
| Chromium i7 Multiplex Kit 10X | 10X Genomics | Cat# 120262 |
| RNAscope Multiplex Fluorescent Reagent Kit v2 | Adv.Cell Diagnostics | Cat# 323100 |
| HiSeq 3000/4000 SBS PE clustering kit | Illumina | Cat# PE-410–001 |
| HiSeq 150 cycle flow cell | Illumina | Cat# FC-410–1002 |
| RNeasy mini kits | Qiagen | Cat# 74104 |
| SuperScript™ IV VILO™ Master Mix with ezDNase™ | Thermo Fisher Sci. | Cat# 11766050 |
| High Sensitivity D5000 Reagents | Agilent | Cat# 5067–5593 |
| High Sensitivity D5000 Screen Tape 4200 Tape Station | Agilent | Cat# 5067–5592 |
| D1000 ScreenTape for 4200 Tape Station | Agilent | Cat# 5067–5582 |
| D1000 Reagents | Agilent | Cat# 5067–5583 |
| Deposited Data | ||
| Raw and processed single-cell RNA sequencing data | This paper | GEO: GSE129798 |
| Experimental Models: Organisms/Strains | ||
| Adult C57BL/6J mice | Jackson Labs | Stock No: 000664 |
| Rosa26tdTomato mice | Jackson Labs | Stock No: 007914 |
| Six2TGC | Kobayashi et al., 2008 | Stock No: 009606 |
| Wnt4-GCE | Kobayashi et al., 2008 | Stock No: 032489 |
| tgHoxb7-Venus | Chi et al., 2009 | Stock No: 016252 |
| Gdf15-CE | McMahon lab | unpublished |
| Oligonucleotides – PCR primers | ||
| Aqp2_F GTGGGAACTCCGGTCCATAG | IDT | https://www.idtdna.com/site/order/oligoentry |
| Aqp2_R CACGGCAATCTGGAGCACAG | IDT | |
| Egr1_F TATGAGCACCTGACCACAGAG | IDT | |
| Egr1_R GCTGGGATAACTCGTCTCCA | IDT | |
| Fos_F AGGGGCAAAGTAGAGCAGCTA | IDT | |
| Fos_R CAATCTCAGTCTGCAACGCA | IDT | |
| Gapdh-F AGGTCGGTGTGAACGGATTTG | IDT | |
| Gapdh-R GTAGACCATGTAGTTGAGGTC | IDT | |
| Hoxb7_F AAGTTCGGTTTTCGCTCCAGG | IDT | |
| Hoxb7_R ACACCCCGGAGAGGTTCTG | IDT | |
| Nphs2_F GACCAGAGGAAGGCATCAAGC | IDT | |
| Nphs2_R GCACAACCTTTATGCAGAACCAG | IDT | |
| Slc12a1_F AGTGCCCAGTAGTGCCAGTC | IDT | |
| Slc12a1_R GTCATAGCACTCCTGATTCC | IDT | |
| Slc12a3_F ACGGCAGCACCTTATACATG | IDT | |
| Slc12a3_R AGGAATGAATGCAGGTCAGC | IDT | |
| Slc34a1_F TGCCTCTGATGCTGGCTTTCC | IDT | |
| Slc34a1_R GATAGGATGGCATTGTCCTTG | IDT | |
| Umod_F TCTGAATGCCACAACAACGC | IDT | |
| Umod_R ACAGGAGCACTTAAACGAGC | IDT | |
| Wnt7b_F TTTGGCGTCCTCTACGTGAAG | IDT | |
| Wnt7b_R TCCCCGATCACAATGATGGC | IDT | |
| Wnt9b_F CTGGTGCTCACCTGAAGCAG | IDT | |
| Wnt9b_R CCGTCTCCTTAAAGCCTCTCTG | IDT | |
| Acsm3_F CTTTGGCCCCAGCAGTAGATG | IDT | |
| Acsm3_R GGCTGTCACTGGCATATTTCAT | IDT | |
| Cyp7b1_F GGAGCCACGACCCTAGATG | IDT | |
| Cyp7b1_R TGCCAAGATAAGGAAGCCAAC | IDT | |
| Prlr_F GAGAAGGGCAAGTCTGAAGAAC | IDT | |
| Prlr_R GGGATGGCATTAGCCGCTC | IDT | |
| Slc22a7_F CAACTGCGGAATCTGGTGCT | IDT | |
| Slc22a7_R ATCAGGCAGGGCACAATGATG | IDT | |
| Slc7a12_F CTCTTGAGAGCACTAGGAGTCT | IDT | |
| Slc7a12_R GTGGTTGCTATCTCTGCATTACA | IDT | |
| Slc7a13_F AGCTGAAGAAACCCAGTAAAACA | IDT | |
| Slc7a13_R GCATCTGAAGAGAGCATTTCCTG | IDT | |
| Recombinant DNA | ||
| GFP-F2A-CREERT2 cassette under control of the Gdf15 locus | McMahon lab | unpublished |
| Software and Algorithms | ||
| TapeStation Analysis Software A.02.02 | Agilent | |
| QuantStudio v1.3 | Applied Biosystems | |
| R Studio v1.1.383 | https://www.rstudio.com/products/rstudio/download/ | |
| R v1.22.0 | CRAN | https://cran.r-project.org/ |
| Seurat v2.3.4 | Butler et al., 2018 |
https://cran.r-project.org/src/contrib/Archive/Seurat/; RRID:SCR_016341 |
| Cell Ranger v2.0 | 10X Genomics | https://support.10xgenomics.com/single-cellgene-expression/software/downloads/latest |
| ggplot2 v3.0 | Wickham |
https://cran.r-project.org/web/packages/ggplot2/index.html RRID:SCR_014601 |
| Matrix v1.2–14 | Bates | http://Matrix.R-forge.R-project.org/ |
| dplyr v0.7.5 | Wickham |
https://github.com/tidyverse/dplyr
RRID:SCR_016708 |
| Star v2.7 | Dobin et al.,2013 |
https://github.com/alexdobin/STAR RRID:SCR_015899 |
| PANTHER v14.1 | Mi et al., 2013 |
http://pantherdb.org/ RRID:SCR_004869 |
| shiny v1.2.0 | Chang et al., 2018 |
https://github.com/rstudio/shiny/releases/tag/v1.2.0 RRID:SCR_001626 |
| VisCello | Packer et al., 2019 | https://github.com/qinzhu/VisCello |
| FlowJo | BD Biosciences |
https://www.flowjo.com/solutions/flowjo/downloads RRID:SCR_008520 |
| Illustrator CC v22.0.1 | Adobe | RRID:SCR_010279 |
| Photoshop CC 19.1.0 | Adobe | RRID:SCR_014199 |
| Excel | Microsoft | |
| LAS X | Lieca | |
| Diva 8.0.2 on Windows 7 | BD Biosciences | |
| Bitplane | Imaris | |
| Other | ||
| Kidney Cell Explorer | This paper | https://cello.shinyapps.io/kidneycellexplorer/ |
| DNA quantification with TapeStation 4200 | Agilent | |
| fast real-time PCR AB7500 | Applied Biosystems | |
| SP8 confocal microscope | Leica | |
| BD SORP FACS Aria IIu [ARIA I] | BD Biosciences | Flow Cytometry Core |
| Vibratome VT1000s | Leica | |
| Cryostat Microm HM550 | ThermoFisher Sci | |
| HiSeq 4000 | Illumina | Translational Genomics Center at Children’s Hospital Los Angeles Center for Personalized Medicine |