| Antibodies |
| SRSF7 Polyclonal Antibody |
Thermo Fisher Scientific |
PA5-39482; RRID:AB_2556056
|
| HAVCR1 Antibody |
R & D Systems |
AF1817; RRID: AB_2116446
|
| Streptavidin, Alexa Fluor 647 conjugate |
Invitrogen |
S21374 |
| SPP1 antibody |
Abcam |
ab218237; RRID: AB_2732079
|
| Tubulin antibody |
Proteintech |
66240; RRID: AB_2881629
|
| Donkey Anti Rabbit, Alexa Fluor 488 conjugate |
Invitrogen |
A21206 |
| Donkey Anti Goat, Alexa Fluor 568 conjugate |
Invitrogen |
A11057 |
| Goat anti-rabbit HRP |
Dako |
P0448 |
| Goat anti-mouse HRP |
Dako |
P0447 |
| Chemicals, peptides, and recombinant proteins |
| 1× DPBS |
Gibco |
14190144 |
| Nuclei EZ Lysis Buffer |
Sigma |
NUC101 |
| Complete ULTRA Tablets, Mini, EDTAfree, EASYpack |
Roche |
05 892 791 001 |
| RNasin Plus Ribonuclease Inhibitors |
Promega |
N2615 |
| SUPERaseIN RNase Inhibitor |
Thermo Fisher Scientific |
AM2696 |
| RNaseZap |
Ambion |
AM9780 |
| RNase free H2O |
Thermo Scientific |
AM9938 |
| Primary RPTEC |
Lonza |
CC-2553 |
| REGM BulletKit |
Lonza |
CC-3190 |
| Glycated albumin |
Sigma |
A8301 |
| Periodic Acid-Schiff (PAS) Kit |
Sigma |
395B |
| siGENOME Human SRSF7 |
Horizon Discovery |
M-015909-01-0020 |
| siGENOME Non-Targeting siRNA |
Horizon Discovery |
D-001210-05-20 |
| Lipofectamine™ RNAiMAX |
Thermo Fisher Scientific |
13778075 |
| Biotinylated Lotus Tetragonolobus Lectin (LTL) |
Vector Laboratories |
B-1325 |
| BCA Protein Assay Kit |
Thermo Fisher Scientific |
23252 |
| Critical commercial assays |
| Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 |
10× Genomics |
PN-1000075 |
| Chromium Single Cell B Chip Kit |
10× Genomics |
PN-1000153 |
|
|
|
| Deposited data |
| Raw and analyzed snRNA-seq data |
This study |
GSE184652 |
| Raw and analyzed bulk RNA-seq data |
This study |
GSE199437 |
|
Data S1 – Source Data
|
This study |
|
| Zenodo data |
This study |
https://zenodo.org/record/6344528
|
| Nuclei isolation protocol |
Protocols.io |
https://dx.doi.org/10.17504/protocols.io.nahdab6
|
| Kidney Interactive Transcriptomics |
The Humphreys Lab |
http://humphreyslab.com/SingleCell/
|
|
|
|
| Experimental models: Organisms/strains |
| BKS.Cg-Dock7m +/− Leprdb/J Leprdb- heterozygous |
The Jackson Lab |
Lot 000642 |
| BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous |
The Jackson Lab |
Lot 000642 |
|
|
|
| Software and algorithms |
| Cell Ranger |
10× Genomics |
https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
|
| Seurat V4.0 |
Satija Lab |
https://github.com/satijalab/seurat
|
| STAR V2.7.3a |
Dubin et al., Bioinformatics 2013 |
|
| CellBender |
Broad Institute |
https://github.com/broadinstitute/CellBender
|
| DoubletFinder V2.0 |
McGinnis et al., Cell Systems 2019
|
https://github.com/chris-mcginnis-ucsf/DoubletFinder
|
| BisqueRNA |
Jew and Alvarez et al et al., Nature Communications 2020
|
https://github.com/cozygene/bisque
|
| scID |
Boufea et al., iScience 2020
|
https://github.com/BatadaLab/scID
|
| MAGMA_Celltyping |
Skene et al., Nature Genetics 2018 |
https://github.com/neurogenomics/MAGMA_Celltyping
|
| CellChat |
Jin et al., Nature Communications 2021
|
https://github.com/sqjin/CellChat
|
| circlize |
Gu et al, Bioinformatics 2014 |
https://jokergoo.github.io/circlize_book/book/
|
| ComplexHeatmap |
Gu et al, Bioinformatcis 2016 |
https://jokergoo.github.io/ComplexHeatmap-reference/book/
|
| COMPASS |
Wagner et al., Cell 2021
|
https://github.com/YosefLab/Compass
|
| fgsea |
Korotkevich et al., bioRxiv 2019 |
https://github.com/ctlab/fgsea
|
| edgeR |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/edgeR.html
|
| topGO |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/topGO.html
|
| plot1cell |
This study |
https://github.com/TheHumphreysLab/plot1cell
|
