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• DIGEST: Dietary Influences on Glucuronidation, a Cross-Sectional Study of Diet and Metabolism

  Plasma samples derived from a study population of control participants (DIGEST: Dietary Influences on Glucuronidation, a Cross-Sectional Study of Diet and Metabolism) were used to profile miRNA circulating in plasma. RNA was isolated from plasma samples using the Qiagen miRNeasy kit. Libraries were prepared using Illumina TruSeq Small RNA Library Prep Kit. Libraries were sequenced on a HiSeq. Data from this sequencing project will be available through dbGaP.

  Study phs003223

• Modelling Multi-Dimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research

  The Center for Cancer Research (CCR), of the intramural NCI undertook a multidimensional clinical genomics study of children and adolescent young adults with relapsed and refractory cancers who were enrolled on other therapeutic trials to determine the feasibility of a genome guided precision therapy protocol in these patients.Note: NCIPM001blood - This sample was previously submitted with study phs002207, with sample ID NCIPM001blood_E and SRR ID SRR18544311.

  Study phs001052

• Genetic Evaluation of Autoinflammatory Diseases

  Many pediatric patients with early-onset autoinflammatory disease (AID) phenotypes are mutation-negative for genetically known AIDs. Recent data suggest a role for Type-I interferon (IFN) dysregulation in causing AID phenotypes with clinical features that are distinct from those found in patients with IL-1 mediated AIDs. We screened patients for the presence of an IFN-response gene signature (IRS) to characterize their clinical phenotypes, IFN-related biomarkers, and genetic causes.

  Study phs001946

• The epigenomic response of skeletal muscle in life-long high-level trained and untrained men and women after acute exercise

  To investigate the influence of lifelong exercise training on the response of skeletal muscle to a bout of acute exercise we generated targeted epigenomic data from long-term endurance (8 men) and strength (8 men) trained individuals and healthy age-matched untrained controls (8 men). Skeletal muscle biopsies were taken from M. vastus lateralis before, directly after, and 3hrs following acute exercise. Control subjects completed one bout of acute endurance exercise and one bout of acute resistance exercise, separated by 4-8 weeks, athletes completed one bout in their respective form of sports. All 96 samples were used for DNA extraction and targeted library construction using a custom Twist Biosciences panel and following EM-methylation tranformation were sequenced (2x150bp paired end) on the Illumina NovaSeq 6000.

  Dataset EGAD50000000512

• RNA sequencing from patient-derived intestinal organoids

  uman duodenal tissues for establishing organoid cultures used in this study were sourced from de-identified surgical specimens (n = 3) of the duodenum obtained from patients who had undergone biopsy procedures unrelated to CeD at Tampere University Hospital. The protocol was approved by the Ethics Committee of Tampere University Hospital, Tampere, Finland (ETL code R18082). RNA from the duodenal organoids was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. RNA purity and concentration were measured using a NanoDrop One spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA). Preparation of the RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Cambridge, UK). Messenger RNA was purified from total RNA using polyA selection and subjected to library construction. Sequencing was performed on an Illumina platform, and 150 bp paired-end reads were generated.

  Dataset EGAD50000000492

• LCM-isolated buccal epithelial cell sequencing

  Single buccal epithelial cells were dissected and collected on an adhesive cap with laser capture microdissection (LCM) with approximately 13-60 cells per cap. Each adhesive cap containing 13-60 cells was independently processed with QIAamp DNA micro kit (Qiagen) for DNA extraction. The NEBNext ultra II FS DNA library kit was used to prepare DNA libraries with low starting material. Paired-end whole genome sequencing reads were obtained with the NovaSeq.

  Study EGAS50000000098

• HGG panel sequencing

  NGS panel sequencing of pediatric high-grade gliomas (HGG), including diffuse midline gliomas and hemispheric HGG. This is a population-based dataset from the Hospital for Sick Children (Toronto, Canada), of patients <18 years of age at diagnosis, and diagnosed between 2000-2022. The goal of the study was to define the genetic drivers in pediatric HGG, including the rates of different genetic drivers, such as H3 and BRAF mutations, in a single-site population based cohort.

  Study EGAS50000000221

• Single-cell RNA sequencing of pediatric Hodgkin Lymphoma to study the inhibition of T cell subtypes

  Here, we applied single-cell RNA-sequencing (scRNA-seq) on isolated HRS cells and the immune cells from the same pediatric classical Hodgkin Lymphoma (cHL) tumors. Specifically, 13 cHL patients and 3 reactive lymph node control samples were included in this cohort. This allowed us to identify genes of cell surface proteins that are consistently overexpressed in HRS cells and can potentially be used as targets for antibody-drug conjugates or CAR T cells. Finally, we identify potential interactions by which HRS cells inhibit T cells, among which the Galectin-1/CD69 and HLA-DRA/LAG3 interactions. However, high levels of inter-patient heterogeneity of the interaction strength were observed. In conclusion, this study identifies new potential therapeutic targets for cHL and highlights the importance of studying heterogeneity when identifying therapy targets.

  Dataset EGAD50000000626

• Transcriptome Sequencing PPGL (2)

  RNA-Seq data (n=81) library preparation was performed as previously reported by Calsina et al 2023 using QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015). The prepared libraries were subsequently sequenced on NovaSeq™ system (Illumina). To combine the new CNIO samples (n=81) with the CNIO+TCGA dataset generated in Calsina et al., 2023, RNA data were processed using ComBat-seq as described in that same article.

  Study EGAS50000000013

• CIDR: Molecular Pathological Epidemiology of Colorectal Cancer

  Colorectal cancer, the second most commonly diagnosed cancer is a biologically heterogeneous disease. To characterize the molecular attributes of colorectal tumors, we conducted targeted sequencing at the Center for Inherited Disease Research (CIDR) on 4,518 tumor and matched normal DNA samples from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and the Colon Cancer Family Registry (CCFR). These consortia are based on cohort and population-based case-control studies.

  Study phs001905