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• Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments

  Dataset EGAD00001001602

• ChIPseq data

  ChIPseq data for H3K4me1 and H3K9me3 in HT29; H3K4me1, H3K27me3, H3K9me3, H3K36me3 in LoVo.

  Dataset EGAD00001003258

• Melanoma and Cancer-Associated Fibroblast Short-Term Cultures Derived from Patient Metastases

  The purpose of this study was to obtain tissue specimens derived from patients with melanoma to generate research tools to advance our understanding of the genetics, pathogenesis, and therapeutics of melanoma. Briefly, tissue was obtained from metastatic lesions and used to generate clonal primary cell lines from melanoma cells and fibroblasts from the tumor microenvironment. RNA was extracted from low passage cell lines using Trizol reagent. cDNA libraries were prepared using the TruSeq mRNA sample preparation kit, v2 (Illumina) and sequenced on the HiSeq 2000 platform (Illumina). The submitted files are bam files that contain both unaligned and aligned reads (human genome, build hg19).

  Study phs001115

• Human lymphoid-neutrophil/monocyte restriction co-ordinately activates increased proliferation despite parallel heterogeneity in transcriptional changes

  Recent studies indicate the human lympho-myeloid restriction process to be a different and more heterogeneous one than historically inferred. Here we describe the development of bulk and clonal culture systems that efficiently support early B-lymphoid differentiation and their use to identify biological and molecular changes that accompany their initial restriction from subsets of CD34+ human cord blood cells with lympho-myeloid-limited potential. Analyses of the changes observed revealed the acquisition of B-lymphoid- and neutrophil/monocyte (NM)-restricted properties are accompanied by a concomitantly accelerated and lineage-shared cell cycling activity and loss of self-renewal properties. Parallel, single-cell transcriptome analysis identified reduced expression of multiple self-renewal-associated genes and an accompanying heterogeneous activation of lineage-regulatory modules during the production of B, NM and dendritic cell precursors. These results uncover a connected regulation of lineage-shared proliferation control with persistent heterogeneity in the biological and transcriptional changes in the same cells undergoing B and NM lineage restriction.

  Study EGAS50000000278

• scRNA-seq of HGSC tumor and ascites

  Immune regulatory metabolites are key features of the tumor microenvironment (TME), yet with a few notable exceptions, their identities remain largely unknown. We uncovered the immune regulatory metabolic states and metabolomes of sorted tumor and stromal, CD4+, and CD8+ cells from the tumor and ascites of patients with high-grade serous ovarian cancer (HGSC) using high-dimensional flow cytometry and metabolomics supplemented with single cell RNA sequencing. Flow cytometry revealed that tumor cells show a consistently greater uptake of glucose than T cells, but similar mitochondrial activity. Cells within the ascites and tumor had pervasive metabolite differences, with a striking enrichment in 1-methylnicotinamide (MNA) in T cells infiltrating the tumor compared to ascites. Despite the elevated levels of MNA in T cells, the expression of nicotinamide N-methyltransferase, the gene encoding the enzyme that catalyses the transfer of a methyl group from S-adenosylmethionine to nicotinamide, was restricted to fibroblasts and tumor cells. Treatment of T cells with MNA resulted in an increase in T cell-mediated secretion of the tumor promoting cytokine tumor necrosis factor alpha. Thus, the TME-derived metabolite MNA contributes to an alternative and non-cell autonomous mechanism of immune modulation of T cells in HGSC. Collectively, uncovering the tumor-T cell metabolome may reveal metabolic vulnerabilities that can be exploited using T cell-based immunotherapies to treat human cancer.

  Study EGAS00001004829

• Genomic and clinical characterization of a familial GIST kindred intolerant to imatinib

  Familial gastrointestinal stromal tumors (GIST) are rare. We present a kindred with multiple family members affected with multifocal GIST who underwent whole genome sequencing of the germline and tumor. Affected individuals with GIST harbored a germline variant found within exon 13 of the KIT gene, (c.1965T>G; p.Asn655Lys, p.N655K) and a variant in the MSR1 gene (c.877C>T; p.Arg293*, pR293X). Multifocal GISTs in the proband and her mother were treated with preoperative imatinib, and resulted in severe intolerance. The clinical features of multifocal GIST, cutaneous mastocytosis, allergies and gut motility disorders seen in the affected individuals may represent manifestations of the multifunctional roles of KIT in interstitial cells of Cajal or mast cells and/or may be suggestive of additional molecular pathways which can contribute to tumorigenesis.

  Study EGAS50000000372

• Identification of molecule relationship between intravenous leiomyomatosis and uterus myoma

  Up to now, there are two hypothesis about the pathogenesis of the relationship of intravenous leiomyomatosis and uterine myoma. One theory suggests that the IVL comes from the smooth muscle cell in the vessel wall.The other theory indicates that the IVL derives from the uterine myometrium. However, limited to the technology, few studies have been deeply explore the underlying relation. In this study, we employ the RNA sequencing to explore the molecule relationship between IVL and uterus myoma. In order to identify the molecule relationship between IVl and uterine myoma we conducted transcriptome sequencing and bioinformaitc analysis

  Dataset EGAD00001003356

• The Genetics of Food Cue Reactivity in Children

  This study aimed to investigate genetic factors related to appetite, eating in the absence of hunger and brain reward response to food cues in a convenience sample of pre-adolescent children taken through two studies (A and B). The study involved genome-wide genotyping using the Illumina Global Screening Array. The study found an obesity polygenic risk score related to parent-reported appetitive traits in children, The study also found that FTO was related to eating in the absence of hunger and brain reward response to food cues. Available data include genotypes, measured height and weight, appetitive traits, consumption, brain reward response to food cues, and sociodemographic variables.

  Study phs003550

• DGCR8 and the six hit, three-step model of schwannomatosis

  In our manuscript, we report the second case of a patient with peripheral schwannomatosis and thyroid alterations cause by the germline pathogenic variant E518K in DGCR8 and analyzed a total of 13 schwannomas from patients in the two kindreds identified up to date. Our analyses revealed how path to tumorigenesis prompted by DGCR8 requires the loss of the wild type allele of Chrm22q and in more than two thirds of the tumors a complete inactivation of NF2.

  Study EGAS00001005665

• Early-life gut microbiome development in preterm infants: the NutriBrain clinical trial

  Metagenomic sequencing data were generated from fecal samples collected from preterm infants enrolled in the NutriBrain clinical trial, a study investigating the impact of early-life nutritional supplementation on gut microbiome development and neurodevelopmental outcomes. Samples were obtained longitudinally during the neonatal period under standardized collection protocols, and total microbial DNA was extracted and subjected to high-throughput shotgun sequencing. The study aims to improve understanding of the relationship between neonatal nutrition, microbiome maturation, and infant health outcomes.

  Study EGAS50000001843

• RNA sequencing data from visceral and abdominal subcutaneous adipose tissue from morbidly obese women with normal glucose tolerance or type 2 diabetes

  The study group consisted of 17 obese women with normal glucose tolerance and 15 obese women with T2DM. Adipose tissue specimens were taken from the epigastric region of the abdominal wall (SAT) and from the major omentum (VAT). RNA was isolated and RNA sequencing was used to analyse the transcriptome. Dharuri H et al, Diabetologia. 2014;57(11):2384-92.

  Study EGAS00001001872

• Dataset for RNA sequencing of Glioblastoma samples

  This dataset contains 10x scRNA sequencing of glioblastoma samples. Sequencing was performed on a Illumina HiSeq 4000. The sequencing was always paired.

  Dataset EGAD50000000081

• DCC_R26.PRAD-CNSM-Array

  Raw Array data from the PRAD-CA for ICGC DCC Release26

  Dataset EGAD00010001414

• DCC_R26.2.PRAD-CNSM-Array

  Raw Array data from the PRAD-CA for ICGC DCC Release27

  Dataset EGAD00010001519

• Rare coding variants in lupus risk genes

  Set of 133 bam files from patients affected with Lupus. BAM alignments for exonic variants present in 76 Lupus-related genes. VCF file describing the variants.

  Dataset EGAD00001004859

• BAM-file spanning the breakpoint region +/- 100kb of Ewing sarcoma

  Extracted regions from WGS of Ewing sarcoma spanning fusion breakpoints +/- 100kb for ctDNA tracking in plasma

  Dataset EGAD00001009110

• Molecular analysis of giant cell lesions

  Giant cell lesions of the jaws are aggressive proliferative conditions that affect young and adult patients. The genetic profile of the tumour has not been established yet. In this project we performed whole exome sequencing of 18 samples and RNAseq (n=6) of giant cell lesions of the jaws. All the tumours are sporadic and only non-syndromic patients were included.

  Study EGAS00001002910

• DAC for a single-cell multi-omic atlas of nodal B-cell non-Hodgkin lymphomas

  Nodal B-cell non-Hodgkin lymphomas (B-NHL) are a clinically diverse set of cancers thought to originate from distinct stages of B-cell maturation. To characterize intratumor heterogeneity across B-NHL entities, we performed CITE-Seq (cellular indexing of transcriptomes and epitopes) on 51 lymph node samples including mantle cell lymphoma (MCL, n = 8), follicular lymphoma (FL, n = 12), germinal center (GCB, n = 5) or activated B-cell (non-GCB/ABC, n = 7) diffuse large B-cell lymphoma (DLBCL) and marginal zone lymphoma (MZL, n = 11) tumors, in addition to non-malignant reactive lymph nodes (rLN, n = 8). We also performed 5 prime scRNA-seq with immune receptor profiling for 11 of these samples (2 rLN, 2 MCL, 3 FL, 2 DLBCL, and 2 MZL).

  Dac EGAC50000000226

• Somatic inflammatory gene mutations accumulate in human ulcerative colitis epithelium

  We performed whole exome sequencing and targeted sequencing of ulcerative colitis with/without colitis associated neoplasm and healthy indivisuals. The aim of this study was to calculate the influence of inflammation and age on a count of genetic mutations in colonic epithelium, and to identify the specific signal pathways on which the significant genetic mutations accumulating in ulcerative colitis patients' colonic epithelium.

  Study JGAS000199

• Mixed_Leukemia_Rearrangement_Screen

  Genomic libraries will be generated from total genomic DNA derived from Mixed Leukemia and MPD samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the illumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000180

• NHLBI TOPMed - NHGRI CCDG: AF Biobank LMU in the context of the MED Biobank LMU

  The Atrial Fibrillation Biobank Ludwig Maximilian University (AFLMU) Study contributes to the spectrum of disease by adding carefully characterized patients with atrial fibrillation. Atrial fibrillation, one of the most common human arrhythmias confers major morbidity, mortality and health care cost, and has been demonstrated to be caused and influenced by genetic and -omics factors. Particularly, AFLMU enrolled patients with an early onset of atrial fibrillation to increase the genetic burden on disease pathophysiology. All patients were recruited applying standardized protocols to maintain homogeneity in data and DNA quality.

  Study phs001543

• The Druze analysis group

  To comprehensively characterize the genetic structure of the Druze population, we recruited and genotyped 40 parent-offspring trios from the Upper Galilee in Israel and the Golan Heights, attempting to capture different extended families (clans) across various geographical locations.

  Study EGAS00001000963

• Whole Genome Sequencing and Variant Calling for Autism Families

  We extracted DNA from whole blood or lymphoblast-derived cell lines and assessed the DNA quality with PicoGreenTM and gel electrophoresis. Whole genome sequencing was performed (Illumina HiSeq2000 and Illumina HiSeq X). WGS reads were mapped to the human reference genome assembly hg19 (GRCh37) using Burrows-Wheeler Aligner v.0.7.12 (TCAG) or Isaac v.2.0.13 (Macrogen). For each genome, we performed local realignment and quality recalibration and detected SNVs and small indels using GATK Haplotype Caller v.3.4.6 without genotype refinement. We detected CNVs using ERDS (estimation by read depth with single nucleotide variants) and CNVnator. We detected structural variants using Manta v.0.29.6. When available by the variant caller (i.e. GATK and Manta), trio-based joint variant calling was conducted for each family.

  Dataset EGAD00001008452

• Understanding human fetal pancreas development using subpopulation sorting and RNA sequencing

  To decipher the populations of cells present in the human fetal pancreas and their lineage relationships, we developed strategies to isolate pancreatic progenitors, endocrine progenitors and endocrine cells. Transcriptome analysis of the individual populationsrevealed a large degree of conservation among vertebrates in the drivers of gene expression changes occurring at different steps of differentiation, althoughnotably, sometimes, different members of the same gene family are expressed. The transcriptome analysis establishes a resource to identify novel genes and pathways involved in human pancreas development. Single cell profiling further captured intermediate stages ofdifferentiation and enabled us to decipher the sequence of transcriptional events occurring during human endocrine differentiation. Furthermore, we evaluate how well individual pancreatic cells derived in vitro from human pluripotent stem cells mirror the natural processoccurring in human fetuses. This comparison uncovers a few differences at the progenitor steps, a convergence at the steps of endocrine induction and the current inability to fully resolve endocrine cell subtypes in vitro.

  Study EGAS00001003127

• Screening for Prostate Cancer-Specific Differentially Methylated Regions Based on MeDIP-seq

  Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) on tissue samples from prostate cancer, benign prostatic hyperplasia (BPH), and bladder cancer.

  Study EGAS50000001894