| Antibodies |
| Anti-Human CD3 BUV661 (clone UCHT1, 1:33 dilution) |
BD Biosciences |
Cat # 612964 |
| Anti-Human CD8 BUV563 (clone RPA-T8, 1:100 dilution) |
BD Biosciences |
Cat # 612914 |
| Rat Anti-CD11b BUV395 (clone M1/70, 1:50 dilution) |
BD Biosciences |
Cat # 565976 |
| Anti-Human CD14 BV750 (clone 63D3, 1:50 dilution) |
BioLegend |
Cat # 367136 |
| Anti-Human CD16 BUV496 (clone 3G8, 1:20 dilution) |
BD Biosciences |
Cat # 612944 |
| Anti-Human CD45 BUV805 (clone HI30, 1:33 dilution) |
BD Biosciences |
Cat # 612892 |
| Anti-Human CD68 BV711 (clone Y1/82A, 1:20 dilution) |
BD Biosciences |
Cat # 565594 |
| Anti-Human CD163 PE/Dazzle (clone GHI/61, 1:20 dilution) |
BioLegend |
Cat # 333624 |
| Anti-Human CD204 APC (clone 7C9C20, 1:20 dilution) |
BioLegend |
Cat # 371906 |
| Anti-Human PVR BV510 (clone SK11.4, 1:20 dilution) |
BioLegend |
Cat # 337634 |
| Anti-Human TIGIT BV605 (clone A15153G, 1:20 dilution) |
BioLegend |
Cat # 372712 |
| Anti-Human PDL1 PercpCy5.5 (clone 29E.2A3, 1:20 dilution) |
BioLegend |
Cat # 329738 |
| Anti-Human PDL2 BV421 (clone 24F.10C12, 1:20 dilution) |
BioLegend |
Cat # 329616 |
| Anti-Human Galectin-9 PE-Cy7 (clone 9M1–3, 1:20 dilution) |
BioLegend |
Cat # 348916 |
| Anti-Human PD1 BV650 (clone EH12.2H7, 1:20 dilution) |
BioLegend |
Cat # 329950 |
| Anti-Human TIM-3 BD BB515 (clone 7D3, 1:50 dilution) |
Biosciences |
Cat # 565568 |
| Anti-Human HLA-DR BV785 (clone L243, 1:20 dilution) |
BioLegend |
Cat # 307642 |
| Anti-Human CD86 BUV737 (clone FUN-1, 1:20 dilution) |
BD Biosciences |
Cat # 612784 |
| Anti-Human CTLA-4 PE-Cy5 (clone BNI3, 1:10 dilution) |
BD Biosciences |
Cat # 555854 |
| Anti-Human TCF1 PE (clone 7F11A10, 1:20 dilution) |
BioLegend |
Cat # 655208 |
| Anti-Human CAIX AF700 (clone 303123, 1:20 dilution) |
R&D Systems |
Cat # FAB2188N-100UG |
| Mouse monoclonal anti-CD8 |
Agilent |
C8/144B |
| Goat monoclonal anti-TIM3 |
R&D biosystems |
AF2365 |
| Mouse monoclonal anti-LAG3 |
LifeSpan Biosciences |
17B4 |
| Mouse monoclonal anti-PD1 |
Gordon Freeman laboratory, Dana Farber Cancer Institute |
EH33 |
| Rabbit Monoclonal anti-CD163 |
Abcam |
EPR19518 |
| Biological Samples |
|
|
| Primary human ccRCC samples |
Dana-Farber/Brigham and Women’s Hospital, Brigham and Women’s Faulkner Hospital, Beth Israel Deaconess Medical Center |
N/A |
| Human adjacent normal tissue samples from ccRCC patients |
Dana-Farber/Brigham and Women’s Hospital, Brigham and Women’s Faulkner Hospital, Beth Israel Deaconess Medical Center |
N/A |
| Human buffy coats |
Research Blood Components, LLC. |
#002 |
| Chemicals, Peptides, and Recombinant Proteins |
| Collagenase D |
Roche |
Cat#11088858001 |
| Dispase (5 Units/mL) |
STEMCELL |
Cat#07913 |
| DNase I (2000 Units/mL) |
New England Biolabs |
Cat#M0303L |
| ACK lysing buffer |
Gibco |
Cat#A1049201 |
| Dynabeads™ MyOne™ SILANE |
Life Technologies |
Cat#2000048 |
| Critical Commercial Assays |
| MACS Dead Cell Removal Kit |
Miltenyi |
Cat#130–090-101 |
| Chromium Single Cell 5’ Library & Gel Bead Kit |
10x Genomics |
Cat#1000006 |
| Chromium Single Cell 5’ Library Construction Kit |
10x Genomics |
Cat#1000020 |
| Chromium Single Cell V(D)J Enrichment Kit, Human T cell |
10x Genomics |
Cat#1000005 |
| Chromium i7 Multiplex Kit |
10x Genomics |
Cat#120262 |
| Chromium Chip A Single Cell Kit |
10x Genomics |
Cat#120236 |
| eBioscience Foxp3 Transcription Factor Staining Buffer Set |
ThermoFisher |
Cat # 00-5523-00 |
| Zombie NIR Fixable Viability Dye |
BioLegend |
Cat # 423106 |
| Deposited Data |
| Data files for scRNA-seq |
This paper |
dbGaP: phs002252.v1.p1 |
| Bulk RNA-seq and clinical data for TCGA KIRC cohort |
TCGA |
https://gdc.cancer.gov/about-data/publications/pancanatlas |
| Bulk RNA-seq and clinical data for CheckMate cohorts |
Braun et al., 2020 |
https://static-content.springer.com/esm/art%3A10.1038%2Fs41591-020-0839-y/MediaObjects/41591_2020_839_MOESM2_ESM.xlsx |
| VDJdb |
Bagaev et al., 2020 |
https://vdjdb.cdr3.net |
| Software and Algorithms |
| Cell Ranger v2.1.0 |
10x Genomics |
http://10xgenomics.com/ |
| GATK4 v2.7.0 |
McKenna et al., 2010 |
https://github.com/gatk-workflows/gatk4-somatic-snvs-indels/ |
| ABSOLUTE v10 |
Carter et al., 2012 |
https://software.broadinstitute.org/cancer/cga/absolute |
| ISAR-GISTIC v1 |
Zack et al., 2013 |
https://hub.docker.com/r/arielyh/erv_pipeline |
| GISTIC2 v1 |
Mermel et al., 2011 |
https://hub.docker.com/r/broadgdac/tool_gistic2 |
| Seurat v3.1.4 |
Butler et al., 2018 |
https://satijalab.org/seurat/ |
| scran v1.12.1 |
Lun et al., 2016 |
https://bioconductor.org/packages/release/bioc/html/scran.html |
| scater v1.12.2 |
McCarthy et al., 2017 |
https://bioconductor.org/packages/release/bioc/html/scater.html |
| batchelor v1.0.1 |
Haghverdi et al., 2018 |
https://bioconductor.org/packages/release/bioc/html/batchelor.html |
| clustree v0.4.3 |
Zappia and Oshlack, 2018 |
https://cran.r-project.org/package=clustree |
| edgeR v3.26.8 |
Robinson et al., 2010 |
https://www.bioconductor.org/packages/release/bioc/html/edgeR.html |
| uwot v0.1.8 |
Mellville et al., 2020 |
https://cran.r-project.org/package=uwot |
| Slingshot v1.7.0 |
Street et al. 2018 |
https://bioconductor.org/packages/release/bioc/html/slingshot.html |
| tradeSeq v1.2.01 |
Van den Berge et al., 2020 |
https://www.bioconductor.org/packages/release/bioc/html/tradeSeq.html |
| CellPhoneDB v2.0 |
Efremova et al., 2020 |
https://github.com/Teichlab/cellphonedb |
| ReactomePA v1.26.0 |
Yu and He, 2016 |
https://bioconductor.org/packages/release/bioc/html/ReactomePA.html |
| survival v3.1–12 |
Comprehensive R Archive Network (CRAN) |
https://cran.r-project.org/package=survival |
| survminer v0.4.3 |
Comprehensive R Archive Network (CRAN) |
https://cran.r-project.org/package=survminer |
| FlowJo v10.7 |
FlowJo LLC. |
https://www.flowjo.com/ |
| HALO platform v3.0 |
Indica Lab |
https://indicalab.com/halo/ |
| FlowSOM v1.21.0 |
Van Gassen et al. 2015 |
http://bioconductor.org/packages/release/bioc/html/FlowSOM.html |
