| Antibodies |
| C8/144B anti-CD8 mouse monoclonal antibody |
Agilent |
Cat# M7103; RRID:AB_2075537 |
| AF2365 anti-TIM3 goat monoclonal antibody |
R and D Systems |
Cat# AF2365; RRID:AB_355235 |
| 17B4 anti-LAG3 mouse monoclonal antibody |
EH33 anti-PD-1 mouse monoclonal antibody |
Cat# LS-B2237; RRID:AB_2249715 |
| EH33 anti-PD-1 mouse monoclonal antibody |
Dr. Morgan Freeman’s laboratory (Dana-Farber Cancer Institute) |
N/A |
| Biological samples |
|
|
| RCC samples profiled by OncoPanel |
Dana-Farber/Brigham and Women’s Hospital |
N/A |
| RCC samples stained by multiplex immunofluorescence |
Dana-Farber/Brigham and Women’s Hospital |
N/A |
| Deposited data |
| 293T cell line experiment RNA-seq data |
This paper |
GSE188885 |
| TCGA KIPAN cohort – mutations, RNA-seq |
TCGA |
https://gdc.cancer.gov/about-data/publications/pancanatlas
|
| TCGA KIPAN cohort – Gene-level copy number calls |
TCGA |
http://firebrowse.org/
|
| TCGA KIPAN cohort – Fusion calls |
TCGA
(Gao et al., 2018) |
https://www.cell.com/cell-reports/fulltext/S2211-1247(18)30395-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124718303954%3Fshowall%3Dtrue
|
| TCGA KIPAN cohort – Arm-level copy number calls, aneuploidy, purity |
TCGA
(Taylor et al., 2018) |
https://www.cell.com/cancer-cell/comments/S1535-6108(18)30111-9
|
| PCAWG kidney cancer cohort |
PCAWG |
https://dcc.icgc.org/releases/PCAWG
|
| IMmotion151 |
(Motzer et al., 2020) |
https://www.cell.com/cancer-cell/fulltext/S1535-6108(20)30542-0
|
| Wang et al. cohort |
(Wang et al., 2020) |
https://onlinelibrary.wiley.com/doi/10.1002/path.5470
|
| Durinck et al. cohort |
(Durinck et al., 2015) |
https://www.nature.com/articles/ng.3146
|
| Malouf et al. cohort |
(Malouf et al., 2014) |
https://clincancerres.aacrjournals.org/content/20/15/4129.long
|
| Sato et al. cohort |
(Sato et al., 2013) |
https://www.nature.com/articles/ng.2699
|
| MSK cohort (pan-RCC) |
(Zehir et al., 2017) |
https://www.nature.com/articles/nm.4333
|
| MSK cohort (tRCC) |
(Marcon et al., 2020) |
https://clincancerres.aacrjournals.org/content/early/2020/05/28/1078-0432.CCR-19-3283.figures-only?versioned=true
|
| Cancer Gene Census (accessed on February 17 2021) |
(Sondka et al., 2018) |
https://cancer.sanger.ac.uk/census
|
| UniProtKB/Swiss-Prot |
https://www.uniprot.org/
|
https://www.uniprot.org/
|
| NCBI Conserved Domain Database v3.19 |
(Marchler-Bauer et al., 2015) |
https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
|
| DEMETER2 Data v6 |
(McFarland et al., 2018) |
https://depmap.org/portal/download/
|
| CRISPR (Avana) Public 21Q1 |
(Dempster et al., 2019) |
https://depmap.org/portal/download/
|
| CTRP v2.0 2015 CTD2
|
(Rees et al., 2016) |
https://depmap.org/portal/download/
|
| Experimental models: Cell lines |
| 293T |
ATCC |
Cat# CRL-3216; RRID:CVCL_0063 |
| UOK109 |
Dr. W. Marston Linehan’s laboratory (National Cancer Institute) |
N/A |
| UOK146 |
Dr. W. Marston Linehan’s laboratory (National Cancer Institute) |
N/A |
| FU-UR-1 |
Dr. Masako Ishiguro’s laboratory (Fukuoka University School of Medicine) |
N/A |
| Software and algorithms |
| Oncotator v1.9.3.0 |
(Ramos et al., 2015) |
https://software.broadinstitute.org/cancer/cga/oncotator
|
| R v3.6.1 |
https://www.r-project.org/
|
https://www.r-project.org/
|
| Python v3.8.5 |
https://www.python.org/
|
https://www.python.org/
|
| Spyder v4.1.5 |
https://www.spyder-ide.org/
|
https://www.spyder-ide.org/
|
| Circos v0.69.9 |
http://circos.ca/
|
http://circos.ca/
|
| GraphPad PRISM 9 |
https://www.graphpad.com/
|
https://www.graphpad.com/
|
| BLAT |
https://genome.ucsc.edu/cgi-bin/hgBlat
|
https://genome.ucsc.edu/cgi-bin/hgBlat
|
| liftOver |
https://genome.ucsc.edu/cgi-bin/hgLiftOver
|
https://genome.ucsc.edu/cgi-bin/hgLiftOver
|
| Enrichr |
https://maayanlab.cloud/Enrichr/#
|
https://maayanlab.cloud/Enrichr/#
|
| Illustrator for Biological Sequences v1.0 |
(Liu et al., 2015) |
http://ibs.biocuckoo.org/
|
| Prion-Like Amino Acid Composition web-based program |
(Lancaster et al., 2014
|
http://plaac.wi.mit.edu/
|
| STAR v2.7.2 |
(Dobin et al., 2013) |
https://github.com/alexdobin/STAR
|
| RSEM v1.3.2 |
(Li and Dewey, 2011) |
https://github.com/deweylab/RSEM
|
| Image J v1.53 |
https://imagej.nih.gov/ij/download.html
|
https://imagej.nih.gov/ij/download.html
|
| Phenochart v1.0 |
https://www.akoyabio.com/support/software/phenochart-whole-slide-viewer/
|
https://www.akoyabio.com/support/software/phenochart-whole-slide-viewer/
|
| Inform v2.2 |
https://www.akoyabio.com/phenoptics/software/inform-tissue-finder/
|
https://www.akoyabio.com/phenoptics/software/inform-tissue-finder/
|
| Indica Lab HALO v3.0 |
https://indicalab.com/halo/
|
https://indicalab.com/halo/
|
| CIBERSORTx |
(Newman et al., 2019) |
https://cibersortx.stanford.edu/
|
