| Biological samples |
|
| Pediatric RCC tumor samples |
Multiple tissue source sites |
See Experimental models and subject details
|
|
| Critical commercial assays |
|
| SureSelectXT Human All Exon V5 Library (without UTRs) |
Agilent |
Cat#5190-6210 |
| TruSeq mRNA Stranded Library Prep Kit |
Illumina |
Cat#20020595 |
|
| Deposited data |
|
| Pediatric RCC WES and bulk RNA-seq data |
This paper |
EGAS00001006057
The genomic landscape of pediatric renal cell carcinoma |
| Processed INFORM RCC cases (INF_KO_00D and RCC544_II) bulk RNA-seq data and WES |
EGAS00001005112
The INFORM Precision Medicine Study for High-Risk Pediatric Malignancies |
EGAS00001005112 |
| Processed INFORM Wilms Tumor German cases bulk RNA-seq data |
EGAS00001005112
The INFORM Precision Medicine Study for High-Risk Pediatric Malignancies |
EGAS00001005112 |
| Processed TARGET Wilms Tumor and normal renal tissue bulk RNA-seq data |
NCI Genomic Data Commons |
https://docs.gdc.cancer.gov/ release 13.0 (September 2018) |
| Processed TCGA KIRC and KIRP projects bulk RNA-seq data |
NCI Genomic Data Commons |
https://docs.gdc.cancer.gov/ release 13.0 (September 2018) |
|
| Software and algorithms |
|
| ANNOVAR |
Wang et al., 2010 |
http://www.openbioinformatics.org/annovar/ |
| Arriba v1.0.1 |
Uhrig et al., 2021 |
https://github.com/suhrig/arriba |
| BEDTools v2.27.1 |
Quinlan and Hall, 2010 |
https://github.com/arq5x/bedtools2 |
| BWA MEM v0.7.15 |
Li, 2013 |
https://github.com/lh3/bwa |
| clusterProfiler v3.16.1 |
Wu et al., 2021 |
https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html |
| CNVkit v0.9.3 |
Talevich et al., 2016 |
https://github.com/etal./cnvkit |
| ComBat-seq/sva v3.36.0 |
Zhang et al., 2020c |
https://github.com/zhangyuqing/ComBat-seq |
| ComplexHeatmap |
Gu et al., 2016 |
https://jokergoo.github.io/ComplexHeatmap-reference/book/ |
| dbplyr v2.1.1 |
n/a |
https://github.com/tidyverse/dbplyr |
| Deseq2 v1.18.1 |
Love et al., 2014 |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| DKFZ IndelCallingWorkflow |
n/a |
https://github.com/DKFZ-ODCF/IndelCallingWorkflow |
| DKFZ SNVCallingWorkflow |
n/a |
https://github.com/DKFZ-ODCF/SNVCallingWorkflow |
| FeatureCounts |
Liao et al., 2014 |
http://subread.sourceforge.net/ |
| ggplot2 v3.3.3 |
n/a |
https://ggplot2.tidyverse.org |
| ggrepel v0.9.1 |
n/a |
https://github.com/slowkow/ggrepel |
| IGV |
Robinson et al., 2011 |
https://software.broadinstitute.org/software/igv/ |
| Platypus |
Rimmer et al., 2014 |
https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data |
| QuanTIseq |
Finotello et al., 2019 |
https://icbi.i-med.ac.at/software/quantiseq/doc/ |
| Roddy |
n/a |
https://github.com/TheRoddyWMS/Roddy |
| Sambamba v0.6.5 |
Tarasov et al., 2015 |
https://github.com/biod/sambamba |
| SAMtools v0.1.19 |
Li et al., 2009 |
RRID:SCR_002105
http://samtools.sourceforge.net/
|
| SOPHIA |
n/a |
https://github.com/DKFZ-ODCF/SophiaWorkflow |
| STAR v2.5.3a |
Dobin et al., 2013 |
RRID:SCR_015899; https://github.com/alexdobin/STAR
|
| TCGA and TARGET RNA-seq data processing |
n/a |
https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline |
| YAPSA v1.16.0 |
Hubschmann et al., 2021 |
https://rdrr.io/bioc/YAPSA/ |
