| Antibodies |
| Anti-ESRP1 rabbit polyclonal antibody |
Sigma Aldrich, Germany |
Altas antibody Cat# HPA023720, AB_1856125 |
| Anti- CD45 antibody |
BioLegend, US |
AB_1236444 |
| Anti- CD326 antibody |
BioLegend, US |
AB_400261 |
| Anti- CD271 antibody |
BioLegend, US |
AB_2282827 |
| Anti- CD26 antibody |
BioLegend, US |
AB_10913814 |
| Anti- CD31 antibody |
BioLegend, US |
AB_2562179 |
| Biological Samples |
|
|
| Primary and metastasis tumor samples and normal samples |
This paper |
|
| Critical Commercial Assays |
| Qiagen AllPrep DNA/RNA/Protein Mini Kit |
|
|
| EnVision Kit |
Dako, Glostrup, Denmark |
Cat#K4003 |
| RNA6000 nano assays |
Agilent |
Cat#5065-4401 |
| RNA Fragmentation Reagents |
Ambion |
Cat#AM8740 |
| Deposited Data |
| Raw sequencing data |
This paper |
EGAS00001002923 |
| Somatic variants |
This paper |
doi:10.17632/6gtrrxrn2c.1
|
| Software and Algorithms |
| R-3.4 |
R Core Team 2017 |
https://www.R-project.org |
| randomForestSRC 2.5.1 |
Ishwaran et al., 2008 |
https://cran.r-project.org/package=randomForestSRC |
| YAPSA |
Huebschmann et al, 2016 |
https://bioconductor.org/packages/YAPSA/ |
| SAMtools |
Li et al., 2009 |
http://www.htslib.org/ |
| Freebayes v1.1.0 |
Garrison et al., 2012 |
https://github.com/ekg/freebayes |
| Sequenza v2.2.0.9000 |
Favero et al., 2015 |
https://bitbucket.org/sequenza_tools/sequenza_canopy) |
| CLICK algorithm |
Sharan et al., 2003 |
http://acgt.cs.tau.ac.il/expander/ |
| Canopy 1.1.1 |
Jiang et al., 2016 |
https://CRAN.R-project.org/package=Canopy |
| PEPCI |
This paper |
http://computational-epigenomics.com/downloads/PEPCI.R |
| DKFZ SNV pipeline |
|
https://doi.org/10.1101/161638 |
| BWA-MEM |
Li, 2013 |
http://bio-bwa.sourceforge.net/ |
| PCAWG delly workflow |
Rausch et al., 2012 |
https://github.com/ICGC-TCGA-PanCancer/pcawg_delly_workflow |
| LUMP algorithm |
Aran et al, 2015 |
www.ncbi.nlm.nih.gov/pubmed/26634437 |
| RnBeads |
Assenov et al., 2014 |
https://bioconductor.org/packages/RnBeads/ |
| EpiAnnotator |
Pageaud et al., 2018 |
http://epigenomics.dkfz.de/EpiAnnotator/ |
| NNLS algorithm |
|
https://cran.r-project.org/web/packages/nnls |
| Houseman algorithm |
Houseman et al., 2012 |
www.ncbi.nlm.nih.gov/pubmed/22568884 |
| edgeR |
Mortazavi et al., 2008; Robinson and Oshlack, 2010
|
http://bioconductor.org/packages/edgeR/ |
| Genomatix software(v3.80116) |
|
http://www.genomatix.de/ |
| PRESCIENT |
This paper |
https://bitbucket.org/weischenfeldt/prescient |
| R package survminer v0.3.1 |
|
https://cran.r-project.org/web/packages/survminer/index.html |
| R package survival v2.41-3 |
Therneau and Grambsch, 2000 |
https://cran.r-project.org/web/packages/survival/index.html |
| Cytoscape v3.4.0 |
|
http://www.cytoscape.org/ |
| |
|
|
| Other |
| Cancer Genome Interpreter drug-variant list |
Tamborero et al, 2018 |
https://www.cancergenomeinterpreter.org/data/cgi_biomarkers_latest.zip |
| H3K27me3, H3K27Ac, H3K4me1, and H3K4me3 ChIP data from LNCaP cells |
Barfeld et al. 2017 |
https://www.ncbi.nlm.nih.gov/m/pubmed/28412251/ |
| Phospho S5 RNA Pol II ChIP data |
Massie et al. 2011 |
https://www.ncbi.nlm.nih.gov/pubmed/21602788 |
| H3K27me3, H3K4me1, H3K27me3 ChIP data from VCaP cells |
Yu et al. 2010 |
https://www.ncbi.nlm.nih.gov/pubmed/20478527 |
| RNA pol II ChIP data from VCaP cells |
Asangani et al. 2014 |
https://www.ncbi.nlm.nih.gov/pubmed/24759320 |
| Ensembl Variant Effect Predictor (VEP) |
|
https://www.ensembl.org/info/docs/tools/vep/index.html |
| Exome Aggregation Consortium(ExAC) |
|
http://exac.broadinstitute.org |
| IARC TP53 database |
|
http://p53.iarc.fr/ |
| ClinVar |
|
https://www.ncbi.nlm.nih.gov/clinvar/ |
| 1000 Genomes Project |
|
http://www.internationalgenome.org |
| NHLBI GO Exome Sequencing Project |
|
https://esp.gs.washington.edu/drupal/ |
| COSMIC database |
|
http://cancer.sanger.ac.uk/cosmic/signatures |
| TCGA-PRAD RNA seq (Downloaded: 05 April 2017) |
|
https://portal.gdc.cancer.gov/ |
| TCGA-PRAD Level 3 SNP-array segmentation (Downloaded: 25 June 2018) |
|
https://portal.gdc.cancer.gov/ |
