| Antibodies |
|
|
| Mouse monoclonal anti-CD8 (C8/144B) |
Cellmarque |
Catalog #108M-96; RRID: AB_1158208 |
| Rabbit monoclonal anti-CD4 (SP35) |
Roche |
Catalog #790-4423 |
| Liquid Concentrated Monoclonal Antibody anti-CD163 |
Leica Biosystems |
Catalog #NCL-L-163; RRID: AB_2756375 |
| Biological Samples |
|
|
| Primary tumor samples |
See Experimental Model and Subject Details
|
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
|
|
| Aprotinin |
Sigma |
Catalog: A6103 |
| Leupeptin |
Roche |
Catalog: 11017101001 |
| Phenylmethylsulfonyl fluoride |
Sigma |
Catalog:93482 |
| Sodium fluoride |
Sigma |
Catalog: S7920 |
| Phosphatase Inhibitor Cocktail 2 |
Sigma |
Catalog: P5726 |
| Phosphatase Inhibitor Cocktail 3 |
Sigma |
Catalog: P0044 |
| Urea |
Sigma |
Catalog: U0631 |
| Tris(hydroxymethyl)aminomethane |
Invitrogen |
Catalog: AM9855G |
| Ethylenediaminetetraacetic acid |
Sigma |
Catalog: E7889 |
| Sodium chloride |
Santa Cruz Biotechnology |
Catalog: sc-295833 |
| PUGNAc |
Sigma |
Catalog: A7229 |
| Dithiothretiol |
ThermoFisher Scientific |
Catalog: 20291 |
| Iodoacetamide |
ThermoFisher Scientific |
Catalog: A3221 |
| Sequencing grade modified trypsin |
Promega |
Catalog: V511X |
| Lysyl endopeptidase, aass spectrometry grade |
Wako Chemicals |
Catalog: 125-05061 |
| Formic acid |
Fisher Chemical |
Catalog: A117-50 |
| Reversed-phase C18 SepPak |
Waters |
Catalog: WAT054925 |
| 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid |
Alfa Aesar |
Catalog: J63218 |
| Tandem mass tags – 10plex |
ThermoFisher Scientific |
Catalog: 90110 |
| Trifluoroacetic acid |
Sigma |
Catalog: 302031 |
| Ammonium Hydroxide solution |
Sigma |
Catalog: 338818 |
| Hydroxylamine solution |
Aldrich |
Catalog: 467804 |
| Ni-NTA agarose beads |
QIAGEN |
Catalog: 30410 |
| Iron (III) chloride |
Sigma |
Catalog:451649 |
| iVIEW DAB Detection Kit |
Roche |
Catalog: 760-091 |
| Bond Polymer Refine Detection Kit |
Leica Biosystems |
Catalog: DS9800 |
| Critical Commercial Assays |
|
|
| TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold |
Illumina |
Catalog: RS-122-2301 |
| Infinium MethylationEPIC Kit |
Illumina |
Catalog: WG-317-1003 |
| Nextera DNA Exosome Kit |
Illumina |
Catalog: 20020617 |
| KAPA Hyper Prep Kit, PCR-free |
Roche |
Catalog: 07962371001 |
| BCA Protein Assay Kit |
ThermoFisher Scientific |
Catalog: 23225 |
| Deposited Data |
|
|
| PhosphoSitePlus |
Hornbeck et al., 2015 |
https://www.phosphosite.org |
| GTEx |
Ardlie et al., 2015 |
https://gtexportal.org/home/ |
| TCGA - ccRCC |
Creighton et al., 2013 |
https://portal.gdc.cancer.gov/ |
| Software and Algorithms |
|
|
| methylationArrayAnalysis (version 3.9) |
Maksimovic et al., 2016 |
https://master.bioconductor.org/packages/release/workflows/html/methylationArrayAnalysis.html |
| Illumina EPIC methylation array (3.9) |
Fortin et al., 2017 |
https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.html |
| VarDict |
Lai et al., 2016 |
https://github.com/AstraZeneca-NGS/VarDict |
| Strelka2 |
Kim et al., 2018 |
https://github.com/Illumina/strelka |
| MUTECT2 |
Cibulskis et al., 2013 |
https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php |
| VarScan2.3.8 |
Koboldt et al., 2012 |
http://varscan.sourceforge.net |
| Pindel0.2.5 |
Ye et al., 2009 |
http://gmt.genome.wustl.edu/packages/pindel/ |
| CNVEX |
Marcin Cieslik Lab |
https://github.com/mctp/cnvex |
| CRISP |
Marcin Cieslik Lab |
https://github.com/mcieslik-mctp/crisp-build |
| Proteowizard |
Kessner et al., 2008 |
http://proteowizard.sourceforge.net/ |
| MSFragger |
Kong et al., 2017 |
https://msfragger.nesvilab.org/ |
| Philosopher |
Alexey Nesvizhskii Lab |
https://philosopher.nesvilab.org/ |
| PeptideProphet |
Keller et al., 2002 |
http://peptideprophet.sourceforge.net/ |
| ProteinProphet |
Nesvizhskii et al., 2003 |
http://proteinprophet.sourceforge.net/prot-proph.pdf |
| PTMProphet |
Deutsch et al., 2015 |
http://www.tppms.org/tools/ptm/ |
| TMT-Integrator |
Alexey Nesvizhskii Lab |
https://github.com/Nesvilab/TMT-Integrator |
| DIA-Umpire |
Tsou et al., 2015 |
https://github.com/Nesvilab/DIA-Umpire |
| msproteomicstools |
http://msproteomicstools.roestlab.org/ |
https://github.com/msproteomicstools |
| ComBat (v3.20.0) |
Johnson et al., 2007 |
https://bioconductor.org/packages/release/bioc/html/sva.html |
| DreamAI |
Pei Wang Lab |
https://github.com/WangLab-MSSM/DreamAI |
| GISTIC2.0 |
Mermel et al., 2011 |
ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTIC_2_0_23.tar.gz |
| iProFun |
Song et al., 2019 |
https://github.com/WangLab-MSSM/iProFun |
| ESTIMATE |
Yoshihara et al., 2013 |
https://bioinformatics.mdanderson.org/public-software/estimate/ |
| WebGestaltR |
Wang et al., 2017 |
http://www.webgestalt.org/ |
| Joint Random Forest |
Petralia et al., 2016 |
https://github.com/WangLab-MSSM/ptmJRF |
| GSVA |
Hänzelmann et al., 2013 |
https://bioconductor.org/packages/release/bioc/html/GSVA.html |
| TCGAbiolinks |
Colaprico et al., 2016 |
http://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html |
| Cytoscape |
Shannon et al., 2003 |
https://cytoscape.org/ |
| TSNet |
Petralia et al., 2018 |
https://github.com/WangLab-MSSM/TSNet |
| xCell |
Aran et al., 2017 |
http://xcell.ucsf.edu/ |
| CPTAC Network Exploration Portal |
Pei Wang Lab |
http://ccrcc.cptac-network-view.org/ |
| CPTAC Data Viewer |
Pei Wang Lab |
http://ccrcc.cptac-data-view.org/ |
| iCAVE |
Liluashvili et al., 2017 |
http://labs.icahn.mssm.edu/gumuslab/software |
| MODMatcher |
Yoo et al., 2014 |
https://github.com/integrativenetworkbiology/Modmatcher |
| ConsensusClusterPlus |
Monti et al., 2003; Wilkerson and Hayes, 2010
|
http://bioconductor.org/packages/release/bioc/html/CancerSubtypes.html |
| OmicsX |
Pan et al., 2019 |
http://bioinfo.wilmer.jhu.edu/OmicsX/ |
| Omic-Sig |
Lih et al., 2019 |
https://github.com/hzhangjhu/Omic-Sig |
| OmicsOne |
Hu et al., 2019 |
https://github.com/HuiZhangLab-JHU/OmicsOne |
| pyQUILTS (v1.0) |
Ruggles et al., 2016 |
http://openslice.fenyolab.org/cgi-bin/pyquilts_cgi.pl |
| MS-GF+ |
Kim and Pevzner, 2014 |
https://github.com/MSGFPlus/msgfplus |
| NeoFlow |
Bing Zhang Lab |
https://github.com/bzhanglab/neoflow |
| netMHCpan |
Jurtz et al., 2017 |
http://www.cbs.dtu.dk/services/NetMHCpan/ |
| Optitype |
Szolek et al., 2014 |
https://github.com/FRED-2/OptiType |
| Customprodbj |
Bing Zhang Lab |
https://github.com/bzhanglab/customprodbj |
| PDV |
Li et al., 2019 |
https://github.com/wenbostar/PDV |
| PeoQuery |
Wen et al., 2019 |
http://pepquery.org |
