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• Pervasive H3K27 acetylation and ERV expression in H3.3K27M gliomas present a therapeutic vulnerability

  We sequenced a total of 2 H3.3K27WT (pcGBM2, G477; 3 replicates total) and 2 H3.3K27M (DIPGVI, DIPGXIII; 6 replicates total) patient-derived cell lines as well as Crispr/Cas9 H3.3K27M-KO clones for one of the cell lines (3 replicates total; DIPGXIII-KO) using ATAC-Seq. P-XX designates passages of replicates. These samples can be found at GEO under accession number GSE128744. This repository contains 1 replicate of G477 to be released under controlled access.

  Dataset EGAD00001004961

• McGill Sperm Methylome Sequencing Data

  The study includes NGS-based WGBS on one sperm DNA sample pooled from 30 participants, and methylC-capture sequencing (MCC-Seq) on the same pooled sperm sample as well as 45 sperm DNA samples derived from both fertile and infertile individuals in two cohorts (Toronto, a fertile cohort; Montreal, an idiopathic infertility cohort). All the data were generated with 100bp paired-end reads using the Illumina HiSeq2000 or 4000 systems.

  Dataset EGAD00001004978

• Panel-based NGS data for ADME genes in human liver samples

  Panel-based next-generation sequencing data of 150 human surgical liver samples from Caucasian donors. The panel was designed for 340 ADME (absorption, distribution, metabolism and excretion) and ADME-related genes. NGS was carried out on the Illumina HiSeq2500 system (Illumina Inc., San Diego, CA, United States) at high depth with 2 × 100 bps paired-end reads. Variants were called using samtools and varscan (2.3.5). Data on n=15,727 filtered variants for the 150 patients are comprised in one vcf file.

  Dataset EGAD00001005116

• RNA sequencing of human intra- and extracranial endothelial cells

  This data set contains the raw .fastq files from one RNA-sequencing experiment. Endothelial cells of the basilar artery and endothelial cells of the carotid artery were post-mortem derived with laser microdissection and sequenced. For this analysis both the basilar- and the carotid artery endothelial cells of eleven individuals were sequenced. For more details please see: DMA Hermkens et al. "Profiling the Unique Protective Properties of Intracranial Arterial Endothelial Cells" Acta Neuropathol Commun. 2019 Oct 14; PMID: 31610812.

  Dataset EGAD00001006203

• PBMC gene expression profiles in diet treated celiac disease upon oral gluten challenge

  This dataset contains PBMC genome-wide RNAseq reads from 21 samples and one expression matrix file after alignment and aggregation of the 21 samples. The samples are case-control drawn on day 6 from long-term GFD treated CD patients after 3 day oral gluten challenge, on day 0 from patient controls on long-term GFD treatment, and on day 6 from 4 week GFD treated healthy controls after 3 day oral gluten challenge.

  Dataset EGAD00001006655

• Detection of Gene Fusions using Targeted Next-Generation Sequencing

  Five commercially available parallel sequencing assays were evaluated for their ability to detect gene fusions in eight cell lines and 18 FFPE tissue samples carrying a variety of known gene fusions. Four RNA-based assays and one DNA-based assay were compared; two were hybrid capture-based, TruSight Tumor 170 Assay (Illumina) and SureSelect XT HS Custom Panel (Agilent), and three were amplicon-based, Archer FusionPlex Lung Panel (ArcherDX), QIAseq RNAscan Custom Panel (Qiagen) and Oncomine Focus Assay (Thermo Fisher Scientific).

  Dataset EGAD00001006913

• WGS data subfolder HFF7VCCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HFF7VCCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001007075

• WGS data subfolder HF3NYCCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HF3NYCCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001008494

• WGS data subfolder HFFWLCCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HFFWLCCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001008495

• Whole genome sequencing of tumor samples from advanced pre-treated NSCLC patients recruited in a phase I/II single-arm trial utilising CVA21, an oncolytic coxsackie virus, in combination with pembrolizumab.

  This dataset contains paired tumor and matched normal whole-genome sequencing (WGS) data from longitudinally collected samples of patients enrolled in an Australian clinical study involving multiple cancer types. For each patient, one or more tumor biopsies were obtained at different treatment time points (Scr, Day 0, Day 15, Day 22, Day 33), and matched normal samples were collected either from blood or non-tumor tissue.

  Dataset EGAD00001015682