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• Genome-wide characterization of Kuwaiti Arab Population

  All the 620 individuals were genotyped using Illumina HumanOmniExpress arrays for 730,525 SNPs.

  Study EGAS00001005034

• RNAseq of whole blood in 359 idiopathic pulmonary arterial hypertension patients reveals biological heterogeneity

  Patients with idiopathic, heritable, or drug-induced pulmonary arterial hypertension (referred to throughout as PAH) were recruited from expert centers across the UK as part of the PAH Cohort study (www.ipahcohort.com). In each case, diagnosis was confirmed by right heart catheterization following established international guidelines, which remained unchanged for the duration of this study. Healthy volunteers were recruited at the same centers and samples processed using the same standard operating procedure at all sites. All individuals gave written, informed consent with local ethical committee approval. Whole blood (3 ml) was collected in Tempus Blood RNA Tubes, and RNAseq was performed using established Illumina methodologies (see online supplement for further details).

  Dataset EGAD00001007981

• HLA sequence data and final calls for VaccGene and 1000Gp3 African populations

  HLA sequence data and final calls for VaccGene and 1000Gp3 African populations

  Dataset EGAD00001011379

• RNA-seq

  Our cohort represents infants with ALL in whom KMT2Ar was not detected by FISH or by standard cytogenetics. Whole-transcriptome sequencing (WTS) libraries were prepared using the NEBNext Ultra II RNA Directional library kit for samples with at least 100ng RNA (n=19), the Clontech double stranded cDNA conversion kit plus the Nextera XT library protocol for samples with less than 100ng RNA (n=4), or ribodepletion using NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) for Total RNA (n=1). Libraries were paired-end sequenced using the Illumina HiSeq 2500.

  Dataset EGAD50000000595

• Large Scale Meta-analysis Characterizes Genetic Architecture for Common Psoriasis-associated Variants

  The genotypes obtained from the Affymetrix Biobank Plus array constituted one of eight Caucasian datasets used in a large genome-wide meta-analysis of the association of psoriasis cases versus unaffected controls. With a combined effective sample size of > 39,000 individuals, this study identified 16 new psoriasis loci achieving genome-wide significance, increasing the total number of identified psoriasis loci for European-ancestry populations to 63.

  Study phs001306

• Sequencing data for oesophageal and related samples - Black et al (WES)

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WES OACs/BOs/normals)

  Dataset EGAD00001011188

• BLUEPRINT: Epigenetic programming during monocyte to macrophage differentiation and trained innate immunity

  Monocyte differentiation into macrophages represents a cornerstone process for host defense. Concomitantly, immunological imprinting of either tolerance or trained immunity determines the functional fate of macrophages and susceptibility to secondary infections. Transcriptomes (RNA-Seq) and epigenomes (ChIP-Seq H3K4me1,H3K4me3,H3K27ac) in four primary cell types: monocytes, in vitro differentiated naive, tolerized and trained macrophages were characterized. Inflammatory and metabolic pathways were modulated in macrophages, including decreased inflammasome activation, and pathways functionally implicated in trained immunity were identified. Strikingly, B-glucan training elicits an exclusive epigenetic signature, revealing a complex network of enhancers and promoters. Analysis of transcription factor motifs in DNase I hypersensitive sites at cell-type specific epigenetic loci unveiled differentiation and treatment specific repertoires. Altogether, this study provides a resource to understand the epigenetic changes that underlie innate immunity in humans.

  Dataset EGAD00001001011

• Cell-free DNA methylation profiling for non-invasive detection and classification of lymphoma

  Compared with traditional tissue biopsies used for lymphoma diagnosis, cell-free DNA methylation profiling offers a minimally invasive approach capable of capturing lymphoma-specific epigenetic alterations. This study investigates genome-wide methylation patterns in plasma using cell-free methylated DNA immunoprecipitation and sequencing (cfMeDIP-seq). Differential methylation analysis of discovery samples identified lymphoma-associated hypermethylated regions that were used to develop classification models for lymphoma detection. Validation analyses demonstrated high accuracy and strong associations between cfDNA methylation scores and independent measures of tumor burden and clinical outcome. These findings support cfDNA methylation profiling as a sensitive approach for non-invasive lymphoma diagnosis.

  Study EGAS50000001463

• RNAseq of jejunum (small intestine) harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 or vehicle

  This experiment consists of RNAseq of jejunum (small intestine) harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 (N = 14) or with vehicle (N = 14).

  Study EGAS00001006584

• Yale Policy for head and neck cancer and HPV clinical trials

  Yale Policy for human controlled access data associated with head and neck cancer and HPV clinical trials

  Dac EGAC50000000403