OpenPBTA: The Open Pediatric Brain Tumor Atlas

. 2023 May 31;3(7):100340. doi: 10.1016/j.xgen.2023.100340

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins

Recover Cell Culture Freezing media	Gibco	Cat# 12648010
Hank’s Balanced Salt Solution (HBSS)	Gibco	Cat# 14175095
Papain	SciQuest	Cat# LS003124
Ovomucoid	SciQuest	Cat# 542000
DNase	Roche	Cat# 10104159001
RNase A	Qiagen	Cat# 19101
100μm cell strainer	Greiner Bio-One	Cat# 542000
DMEM/F-12 medium	Sigma	Cat# D8062
Fetal Bovine Serum (FBS)	Hyclone	Cat# SH30910.03
GlutaMAX	Gibco	Cat# 35050061
Penicillin/Streptomycin-Amphotericin B	Lonza	Cat# 17-745E
Normocin	Invivogen	Cat# ant-nr-2
B-27 supplement minus vitamin A	Gibco	Cat# 12587-010
N-2 supplement	Gibco	Cat# 17502001
Epidermal growth factor	Gibco	Cat# PHG0311L
Basic fibroblast growth factor	PeproTech	Cat# 100-18B
Heparin	Sigma	Cat# H3149

Critical commercial assays

GenePrint 24 STR profiling kit	Promega	Cat# B1870
DNA/RNA AllPrep Kit	Qiagen	Cat# 80204
TruSeq RNA Sample Prep Kit	Illumina	Cat# FC-122-1001
KAPA Library Preparation Kit	Roche	Cat# KK8201
AllPrep DNA/RNA/miRNA Universal kit	Qiagen	Cat# 80224
QIAsymphony DSP DNA Midi Kit	Qiagen	Cat# 937255
KAPA Hyper-Prep kit	Roche	Cat# 08098107702
RiboErase kit	Roche	Cat# 07962304001

Deposited data

Raw and harmonized WGS, WXS, Panel, RNA-Seq	KidsFirst Data Resource Center, This project	Open Pediatric Brain Tumor Atlas et al.⁷⁹
Merged summary files	This project	https://cavatica.sbgenomics.com/u/cavatica/openpbta
Merged summary files and downstream analyses	This project	https://github.com/AlexsLemonade/OpenPBTA-analysis ⁸⁰
Processed data	This project	https://pedcbioportal.kidsfirstdrc.org/study/summary?id=openpbta
Data underlying figures and molecular alterations	This project	Shapiro et al.⁸¹

Experimental models: Cell lines

CBTN pediatric brain tumor-derived cell lines	Ijaz et al.¹³	See Table S1 for identifiers

Software and algorithms

Data processing and analysis software	Multiple	See Table S5 for identifiers
OpenPBTA workflows repository	This project	https://github.com/d3b-center/OpenPBTA-workflows ⁸²
OpenPBTA analysis repository	This project	https://github.com/AlexsLemonade/OpenPBTA-analysis ⁸⁰
OpenPBTA manuscript repository	This project	https://github.com/AlexsLemonade/OpenPBTA-manuscript

Other

TCGA WXS dataset	NIH The Cancer Genome Atlas (TCGA)	dbGAP: phs000178.v11.p8
Cancer hotspots	MSKCC	https://www.cancerhotspots.org/#/download (v2)
Reference genomes	Broad Institute	https://s3.console.aws.amazon.com/s3/buckets/broad-references/hg38/v0/
Reference genome hg38, patch release 12	UCSC	http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/
Human Cytoband file	UCSC	http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz
CDS from GENCODE v27 annotation	GENCODE	https://www.gencodegenes.org/human/release_27.html
PFAM domains and locations	UCSC	http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/pfamDesc.txt.gz; https://pfam.xfam.org/family/PF07714
BSgenome.Hsapiens.UCSC.hg38 annotations	Bioconductor	https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html
gnomAD v2.1.1 (exome and genome)	Genome Aggregation Database	https://gnomad.broadinstitute.org/downloads#v2-liftover-variants
KEGG MMR gene set v7.5.1	Broad Institute	https://www.gsea-msigdb.org/gsea/msigdb/download_geneset.jsp?geneSetName=KEGG_MISMATCH_REPAIR
ClinVar Database (2022-05-07)	NCBI	https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2022/clinvar_20220507.vcf.gz