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• 300-Obese: clinical cohort of obese individuals, Nijmegen, the Netherlands

  300-Obese cohort was recruited at the Radboud University Medical Center (RUMC), Nijmegen, the Netherlands. The cohort comprises 377 participants included by the following criteria: age>55 years, BMI>27 kg/m2. The cohort data includes gut microbiome, NMR serum metabolomics, deep cardiovascular phenotyping and broad range of phenotypic information.

  Study EGAS00001003508

• 112 "KOREAN" never-smoker female adenocarcinoma exome-seq

  All sequencing was performed within the DNAlink (Korea) by using the Solexa sequencing technology (Illumina, San Diego, CA). 1 ug of genomic DNA was sheared to an average size of 150 bp by using the Covaris System. The libraries were prepared by using TruSeq DNA Sample Prep Kit (Illumina). The purified DNA library was hybridized with the SureSelect Human All Exon V3 probe set (Agilent Technologies) to capture 50 Mb of targeted exons following the manufacturer’s instructions. Exome capture was carried out using the Agilent SureSelect Human All Exon 50Mb Kit. The captured exome libraries were sequenced on the Illumina HiSeq2000 using the manufacturer’s recommended protocols.

  Dataset EGAD00001005126

• Indonesian sea-nomads genomic history

  This study observes the origin of the last living sea nomad group in Indonesia using genome-wide SNP data, and tracks their dispersal in the archipelago. This study involves new samples on not only the sea nomad group, but also surrounding populations where the sea nomad settled. We revealed the scenario of their origin and unique admixture patterns during their dispersal and re-settlement.

  Study EGAS00001002246

• Platinum-based chemotherapy induces opposing effects on immunotherapy response-related spatial and stromal biomarkers in the bladder cancer microenvironment

  The goal of the current project was to investigate the modulation of the tumor-immune microenvironment (TME) by neo-adjuvant platinum-based chemotherapy in muscle-invasive bladder cancer. Furthermore, we aimed to focus on how this modulation affects biomarkers of response to immune checkpoint inhibitors. Additionally, we aimed to explore the differences between MVAC and gemcitabine-containing platinum-based regimens regarding their effects on the bladder TME.

  Study EGAS50000000309

• Detection of maternal DNA contamination in the placenta

  We use whole-genome sequencing of monozygotic (and dizygotic) twins to detect somatic mutations to infer the cellular history of the twinning event. We recruited monozygotic twins with varying degrees of fetal membranes to compare the twinning events between theses subsets. We used blood, buccal epithelial cell, placenta, and umbilical cord to trace the embryonic somatic mutations. Using the somatic mutations from various tissues we infer the approximate timing of twinning in each monozygotic twin subtypes.

  Study EGAS00001006155

• Targeted exome sequencing identify compound heterozygous TYK2 mutations in patients with primary immunodeficiency who developed EBV-associated lymphoma

  In this study, we evaluated 2 siblings with primary immunodeficiency who developed EBV-associated lymphoma. Immunophenotyping of PBMCs revealed that both patients had significant T cell lymphopenia characterized by low na?ve CD4+ T cell counts. To identify the causative genetic mutations in the patients, we performed targeted exome sequencing using the Illumina MiSeq on the patients and their parents. The results showed a novel compound heterozygous mutations in the gene encoding tyrosine kinase 2 (TYK2) in the patients.

  Study JGAS000098

• H3K27ac ChIP-seq in primary inflammatory (TPP) macrophages

  We investigated an intergenic haplotype on chr21q22, linked to five different inflammatory diseases, and identified the molecular mechanism by which the risk haplotype increases expression of the causal gene, ETS2. This mechanism was predicted to alter enhancer activity at the disease-associated locus. We therefore performed H3K27ac ChIP-seq in inflammatory macrophages from minor and major allele homozygotes at the causal allele and investigated the effect on enhancer activity. In doing so, we mechanistically delineated how the risk haplotype increases expression of ETS2.

  Study EGAS00001007562

• GenomeAsia 100K Project: Human DNA samples collecting and whole genome sequencing of Asian populations

  The number of basal divergences, admixture, and the degrees of isolation among Indigenous North Eurasian and Native South American populations remain debated, with most insights derived from genome-wide genotyping data. This study aims to improve our understanding of the ancient dynamics and shaping of the contemporary populations of North Eurasia and the Americas. Using large-scale whole-genome sequencing of 1,537 individuals across 139 ethnic groups from these regions, we identify population structures, clarify the prehistoric migrations and the role of past environments in the diversification of human populations.

  Study JGAS000781

• Understanding_the_multicellular_dynamics_of_clear_cell_renal_cell_carcinoma___visium

  This study will reconstruct the single cellular phylogeny of tumour and immune cells in relation to both genomic, functional, and spatial location. 20 tumours in total will be studied, including non-progressing small renal masses, progressing small renal masses, relatively indolent larger tumours, and high risk tumour with metastatic sampling. We aim to: Generate a focused, comprehensive phylogenetic characterisation of tumour cells Understand the dependencies of the cancer genome, transcriptome, tissue architecture and the single cellular micro-environment Quantify the single cellular composition and functional intra- and inter- tumoural heterogeneity Determine the phylogeny of tumour associated lymphocytes and their relationship to neo-epitopes and the immune microenvironment Investigate the mechanisms by which the tumour-normal interface constrains tumoural growth.

  Study EGAS00001006045

• Single-cell profiling of the leukemic and non-leukemic immune cell compartments in CD8+ T-cell Large Granular Lymphocytic Leukemia

  We performed a detailed and precise characterisation of the clonally expanded leukemic cells in CD8+ T cell Large Granular Lymphocytic Leukemia (T-LGLL). By combining scRNA+TCRαβ-seq with bulk RNA sequencing data we showed evidence of a strong antigen-driven immune response that shapes the entire immune cell repertoire in T-LGLL. Our study highlights how the whole immune cell repertoire including the hyperexpanded CD8+ T-LGLL cells, the non-leukemic CD8+ cells, CD4+ cells, and monocytes contribute to the CD8+ T-LGLL disease phenotype. Please note that this submission contains the fastq files while the processed count matrices can be found in ArrayExpress by the accession E-MTAB-11170.

  Study EGAS00001005297

• Spatiotemporal single-cell analysis reveals a time-dependent immunological modulation by multi-fractionated radiotherapy in esophageal cancer

  Description Here, by integrative spatial and single-cell analyses using spatial transcriptome (VISIUM) and single-cell RNA sequencing (scRNA-seq), we examined the spatiotemporal dynamics of immune-response in the tumor microenvironment of esophageal squamous cell carcinoma (ESCC) before, during and after RT. The comprehensive single-cell analyses demonstrated the infiltration of immune cells into tumor with the dynamic change of immune-stimulatory and -suppressive gene expression after RT. ScRNA-seq analysis uncovered the time- and cell-type-dependent alteration of gene expression profile from during to after RT. This datasets in the present study will provide the information of RT-induced gene signature to seek an appropriate target of personalized immunotherapy combined with radiotherapy and of determining the timing of the combination therapy.

  Study JGAS000712

• Adrenal scRNA sequencing data access

  Raw sequencing datasets for manuscript "Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution".

  Dac EGAC50000000869

• LOGGIC Core BioClinical Data Bank: Added clinical value of RNA-Seq in an international molecular diagnostic registry for pediatric low-grade glioma patients

  Study EGAS00001007072

• G3-MB ATAC Sequencing

  ATAC sequencing for two MYC-amplified G3-MB cell models.

  Dataset EGAD50000002305

• G3-MB WGS

  Whole genome sequencing BAM files for four samples of MYC-amplified Group 3 medulloblastoma cell models.

  Dataset EGAD50000002302

• SMPaeds tumour tissue lcWGS

  Low coverage whole genome sequencing (0.5-4X) for both relapse and archival diagnostic tumour tissue.

  Dataset EGAD50000000784

• Batch1-2_Genotypes_PostQC

  Combined genotypes for Batch 1 and 2 after quality control. All individuals included in analyses.

  Dataset EGAD00010002127

• Hessequa-descendants Genome-wide SNP data

  Genome-wide data for population genetics analyses

  Dataset EGAD00010002113

• scoop-G-1

  Human Core Exome Genotyping for 1456 severe early onset obesity cases (SCOOP)

  Dataset EGAD00010001623

• GWAS results from Danjou et al, Nature Genetics 2015

  GWAS results in epacts format for Danjou et al, Nature Genetics 2015

  Dataset EGAD00010001722

• ADME_gene_expression

  Gene expression for 303 ADME and ADME related genes (averaged log2 signal intensities using Human-WG6v2 Expression BeadChip)

  Dataset EGAD00010001709

• EGAD00010000498

  Affymetrix SNP6.0 genotype data for prostate cancer patients

  Dataset EGAD00010000498

• 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

• Reference epigenome OB56_N_PreA_mRNA-Seq data generated from KEP study

  A OB56_N_PreA_mRNA-Seq paired end data for Preadipocytes(fat)

  Dataset EGAD00001003486