KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical Commercial Assays
KAPA HiFi DNA Polymerase	Kapa Biosystems	KK2612
Agencourt AMPure XP beads	Beckman Coulter	A63882
SeqCap EZ HGSC VCRome Kit v 2.1	Roche	06266380001
TruSeq SBS kit v3 HS	Illumina	FC-401-3001
Oligo(dT)25 Dynabeads	Life Technologies	61002
ERCC spike-in mix #1	Ambion, Life Technologies	4456740
NEBNext RNA First Strand Synthesis Module	New England Biolabs	E7525S
NEBNext Ultra Directional RNA Second Strand Synthesis Module	New England Biolabs	E7550S
Uracil-DNA Glycosylase	New England Biolabs	M0280L
Phusion High-Fidelity PCR Master Mix	New England Biolabs	M0531L
Infinium OmniExpress-24 Kit	Illumina	WG-315-1101
GenePrint24 System for STR Typing	Promega	B1870
Investigator Quantiplex Kit	QIAGEN	387018
PrimeTime Gene Expression 2x qPCR mix	IDT	1055772
Deposited Data
WES human and mouse BAM files	This paper	dbGAP phs001437
RNA-Seq human and mouse BAM files	This paper	dbGAP phs001437
Intermediate files	This paper	https://figshare.com/projects/Genomic_landscape_of_childhood_cancer_patient-derived_xenograft_models/38147
Processed data – somatic mutations, gene expression, RNA fusions, segmentation files, focal copy number	This paper	https://pedcbioportal.org/login.jsp#summary
Processed data – SNP array-associated analyses files, FPKM matrix, WES MAF files	This paper	Figshare
HapMap 3 draft release 2	International HapMap project	ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/latest_phaseIII_ncbi_b36/plink_format/
Experimental Models: Organisms/Strains
261 pediatric PDX models	This paper	Table S1
Oligonucleotides
Human PTGER2 qPCR FWD primer, 5′-GCTGCTTCTCATTGTCTCGG-3′	IDT	custom
Human PTGER2 qPCR REV primer, 5′-GCCAGGAGAATGAGGTGGTC-3′	IDT	custom
Human pTGER2 qPCR probe, 5′-FAM-CAGTGTCATTCTCAACCTCATCCGCA-IOWA-BLACK-3′	IDT	custom
Mouse pTGER2 qPCR FWD primer, 5′-ACATCAGCGTTATCCTCAACC-3′	IDT	custom
Mouse pTGER2 qPCR REV primer, 5′-GCTACTGCCAGACAATCCG-3′	IDT	custom
Mouse pTGER2 qPCR probe, 5′-TXRED-TCATTCGCATGCACCGTCGGA-IOWA-BLACK-3′	IDT	custom
Software and Algorithms
FusionCatcher 0.99.7b	Nicorici et al., 2014	https://github.com/ndaniel/fusioncatcher
STAR-Fusion 1.1.0	Haas et al., 2017	https://github.com/STAR-Fusion
STAR 2.5.2b	Dobin et al., 2013	https://github.com/alexdobin/STAR
RSEM 1.2.28	Li and Dewey, 2011	https://github.com/deweylab/RSEM
TumorMap 1.0	Newton et al., 2017	https://tumormap.ucsc.edu/
Stan 2.16.0	Carpenter et al., 2017	https://github.com/stan-dev/cmdstan
Fgsea 1.5.1	Sergushichev, 2016	https://bioconductor.org/packages/release/bioc/html/fgsea.html
Pandas 0.23.0	McKinney, 2010	https://pandas.pydata.org/
R, various	R Core Team	http://www.R-project.org/
Python 3.6.5	Python Core Team	https://www.python.org/
Jupyter 1.0.0	Kluyver et al., 2016	https://jupyter.org/index.html
Seaborn 0.8.1	Seaborn Core Team	https://seaborn.pydata.org/
Maftools 2.0.15	Mayakonda et al., 2018	https://github.com/PoisonAlien/maftools
R 3.4.3	R Core Team	http://www.R-project.org/
ComplexHeatmap 2.1.0	Gu et al., 2016	https://www.bioconductor.org/packages/3.7/bioc/html/ComplexHeatmap.html
deconstructSigs 1.8.0	Rosenthal et al., 2016	https://github.com/raerose01/deconstructSigs
Nexus 8.0	Biodiscovery	https://www.biodiscovery.com/
GISTIC 2.0.23	Mermel et al., 2011	https://www.broadinstitute.org/node/358411
MutSigCV 1.3.01	Lawrence et al., 2013	http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/MutSigCV
HGSC Mercury 3.2	Reid et al., 2014	https://www.hgsc.bcm.edu/software/mercury
BWA 0.7.17-r1188	Li and Durbin, 2010	http://bio-bwa.sourceforge.net/
GATK 3.8.1	McKenna et al., 2010	https://www.broadinstitute.org/gatk/
PLINK 1.9	Chang et al., 2015	https://www.cog-genomics.org/plink/1.9/
PLINK 1.07	Purcell et al., 2007	http://zzz.bwh.harvard.edu/plink/
Samtools 1.9	Li et al., 2009	http://samtools.sourceforge.net/
Sambamba 0.6.6	Tarasov et al., 2015	https://github.com/biod/sambamba
Picard 2.18.14-0	2018	https://github.com/broadinstitute/picard
Cufflinks 2.2.1	Trapnell et al., 2010	https://github.com/cole-trapnell-lab/cufflinks
RNA-SeQC 1.1.8	Deluca et al., 2012	https://github.com/broadinstitute/rnaseqc
AlignStats 0.3	BCM-HGSC	https://github.com/jfarek/alignstats
SOAPFuse 1.26	Jia et al., 2013	https://sourceforge.net/projects/soapfuse/
HTSeq 0.9.1	Anders et al., 2015	https://github.com/simon-anders/htseq
Pindel 0.2.5b5	Ye et al., 2009	https://github.com/genome/pindel
deFuse 0.7.0	McPherson et al., 2011	https://github.com/amcpherson/defuse
Bamutil 1.0.14	Jun et al., 2015	https://github.com/statgen/bamUtil
Trinity 2.5.1	Grabherr et al., 2011	https://github.com/trinityrnaseq/trinityrnaseq
Strelka 2.9.2	Kim et al., 2018b	https://github.com/Illumina/strelka
NGSCheckmate 1.0	Lee et al., 2017	https://github.com/parklab/NGSCheckMate
Other
TARGET pediatric tumors RNA-sequencing dataset	The TARGET Consortium	https://ocg.cancer.gov/programs/target/data-matrix
GTEx normal tissues RNA-sequencing dataset	The GTEx Consortium. 2013	http://www.gtexportal.org/home/index.html
Exome Aggregation Consortium 0.3.1	Lek et al., 2016	http://exac.broadinstitute.org/
The International Genome Sample Resource and 1000 genomes project	Birney and Soranzo, 2015	https://www.internationalgenome.org/
NHBLI Exome Sequencing Project (ESP)	Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP), Seattle, WA (URL: http://evs.gs.washington.edu/EVS/) [date (month, year) accessed].	http://evs.gs.washington.edu/EVS/