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• Dataset Plasma-seq

  We performed low coverage whole genome sequencing of plasma DNA from prostate cancer patients to establish copy number profiles on both a genome-wide and a gene-specific level. The data include plasma samples from prostate cacner patients (n=13), non-malignant controls (males, n=10 and females, n=9), plasma samples from pregnancies with aneuploid and euploid fetuses (n=4). Furthermore, we sequenced different tumor samples (n=6) of one patients and a serial dilution of HT29 in a background of normal DNA (n=9).

  Dataset EGAD00001000364

• 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

• WGS and WES of Advance Prostate Cancer

  The dataset consists of BAM files of 2 pairs of matched tumor/normal samples of a men with advanced prostate cancer. One pair is whole genome sequencing: WGS_T/WGS_N for tumor and normal samples, respectively; and the other pair is whole exome sequencing: WES_T/WES_N for tumor and normal specimens, respectively. Details can be found at the publication titled: "Molecular Medicine Tumor Board: Whole Genome Sequencing to Inform on Personalized Medicine for a Man with Advanced Prostate Cancer"

  Dataset EGAD00001006487

• 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

• Genome Sequencing of Hepatocellular Carcinoma at The Human Genome Sequencing Center of Baylor College of Medicine (HGSC-BCM)

  Hepatocellular carcinoma (HCC) accounts for 85-90% of primary liver cancers. We have focused on three major HCC etiologies:hepatitis C virus (HCV), hepatitis B virus (HBV), and nonviral causes. The onset and progression of cancer is driven by extensive rearrangement and mutation of the genome. We combined our capability to capture and enrich exome DNA with the next generation sequencing capacity to allow us to detect and characterize the somatic mutation profile of patients with HCC. Patient samples were collected by the Liver Center, Division of Abdominal Transplantation in the Baylor College of Medicine Department of Surgery. Sequencing of HCC is one of the NHGRI Center Initiated Projects in progress in the Human Genome Sequencing Center at Baylor College of Medicine.

  Study phs000509

• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): Large Scale Flu Surveillance Study (LSFS)

  The purpose of this study was to better understand behavioral and physiological functioning in relation to recent self-reported influenza and influenza-like-illness (ILI), including coronavirus disease (COVID-19). Over 65,000 Achievement members responded to a weekly one-click survey asking if they had experienced ILI within the previous 7-day period. If they responded no, they were given the option to complete a survey about their risk factors and behavior. If they responded yes, they were given the option to complete a survey asking about the specifics of the incident. Participants were also asked to sync their wearable activity trackers and health apps in order for researchers to better understand changes in behavioral and physiological outcomes related to self-reported ILI experiences.DOI: https://rapids.ll.mit.edu/10.57895/fkth-d352

  Study phs002539