DAC

Data access agreement for ATRT

Dac ID Contact Person Email Access Information
EGAC00001000306 Annie Huang annie [dot] huang [at] sickkids [dot] ca No additional information is available

This DAC controls 17 datasets:

Dataset ID Description Technology Samples
EGAD00001004576 ATRT whole exome sequencing Illumina HiSeq 2000,unspecified 32
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
EGAD00001004836 ATRT ChIPSeq H3K27ac Illumina HiSeq 2500 3
EGAD00001004837 ATRT RNASeq Illumina HiSeq 2500 4
EGAD00001004847 ATRT ATACSeq Illumina HiSeq 2000 18
EGAD00010000710 ATRT genotyping blood 0
EGAD00010000712 ATRT genotyping 0
EGAD00010000789 ATRT expression Illumina Human HT6-v3 Array,unknown 4
EGAD00010000790 ATRT expression Illumina Human HT6-v3 Array,unknown 41
EGAD00010001433 ATRT methylation Illumina HumanMethylation450 BeadChip 0
EGAD00010001546 ATRT expression Illumina HumanHT-12 v4.0 Array 43
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 manufacturer’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 manufacturer’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