Paediatric Tumour Profiling - EGA European Genome-Phenome Archive

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Dataset ID	Description	Technology	Samples
EGAD00001004802	ETMR RIPSeq	Illumina HiSeq 2000	2
EGAD00001004803	RNA was prepared using the IlluminaTruSeq RNA sample preparation kit for poly-adenylated mRNA with an average of 97.64 million reads per sample respectively	Illumina HiSeq 2000	5
EGAD00001004805	ATACSeq library amplification was performed on 5 ETMR tumour samples using the NEBnext High Fidelity 2xPCR Master Mix (New England Biolabs, Cat#M0541S) according to the manufacturer’s protocol. ATAC-seq libraries were sequenced using single-end 50 bp reads on the Illumina HiSeq 2000 platform. ATAC-seq peaks analysed was conducted as published previously(Torchia et al. 2016).	Illumina HiSeq 2000	8
EGAD00001004809	H3K27Ac ChIP-seq DNA libraries for 5 ETMR samples were prepared using NEBNext ChIP-seq Illumina Sequencing library preparation kit. ChIP-seqlibraries were sequenced using single-end 50 bp reads on the Illumina HiSeq 2000 platform. ChIP-seq peaks analysed was conducted as published previously(Torchia et al. 2016).	Illumina HiSeq 2000	10
EGAD00010001667	33 ETMR samples were genotyped using Illumina HumanOmni2.5M array. Hybridization and scanning was done according to the manufacturer's instructions (Illumina). Copy number (Log R) and B allele frequency estimates were obtained sing the Genotyping module (v1.9.4) in GenomeStudio v2011.1 (Illumina). Normalized and log2-transformed copy number measurements were imported from genomestudio and analysed using R package CopyNumber to identify segments with similar copy number.	Illumina Omni2.5	33
EGAD00010001669	77 ETMR samples were profiled using methylation array. DNA from frozen tissue and formalin-fixed, paraffin-embedded (FFPE) materials were analyzed with the Illumina Infinium HumanMethylation450 (450k) and MethylationEPIC (EPIC) array according to manufacturerâ€™s instructions and with a modified method that was previously described (Torchia et al. Cancer Cell. 2016; Triche et al. Nucleic Acids Res. 2013).	Illumina Infinium HumanMethylation450K	77
EGAD00010001701	Total RNA (100ng) from 21 ETMRs with C19MC structural alterations and 28 other PBTs was prepared with nCounter miRNA Sample Prep Kit according to standard protocol. miRNA expression profiling was conducted with human v1, v2, or v3 miRNA panel on nCounter miRNA expression platform (NanoString Technologies, Seattle, WA) according to manufacturerâ€™s protocol. Signal normalization was done using nSolver Analysis and batch corrected using ComBat (Johnson et al. Biostatistics. 2007). 565 miRNAs overlapped between all three versions and was used for further analyses. Fold change and supervised t-test with FDR correction was calculated between the ETMRs and other PBTs.	Nanostring	49