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• Transcriptomic signatures of CD4+ T cells from visceral leishmaniasis (VL) patients

  Bulk RNA-sequencing was performed on CD4+ T cells isolated from the blood of visceral leishmaniasis patients (n = 12) and endemic controls (EC; n = 12). CD4+ T cells were obtained by magnetic-activated cell sorting (MACS). Alterations in the transcripts of T helper (Th) cells during infection were identified.

  Dataset EGAD00001005807

• LBC1936 VCF

  LBC1921 and LBC1936 GVCFs called with GATK's HaplotypeCaller were combined and subject to variant quality score recalibration. This VCF contains the subset of samples (n = 1068) from the LBC1936 cohort.

  Dataset EGAD00001005478

• Single-cell TCR sequencing of DQ2.2-glut-L1-specific T cells

  In order to characterize the T cell receptor (TCR) repertoire of DQ2.2-glut-L1-specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-α and TCR-β genes of the single HLA-DQ2.2:DQ2.2-glut-L1 tetramer binding CD4+ T cells isolated from six T-cell lines (TCLs) of four Celiac disease patients.

  Dataset EGAD00001005047

• Exome sequencing of 277 rainforest hunter-gatherers and neighbouring farmers from Central Africa

  Exome sequencing of 277 rainforest hunter-gatherers (RHG) and neighbouring farmers (AGR) from Central Africa was performed based on the Nextera Rapid Capture Expanded Exome Kit (62-Mb content) with the Illumina HiSeq 2500. After QC filters, exomes of 266 unrelated individuals were obtained at high coverage (Lopez et al., Curr Biol 2019).

  Dataset EGAD00001005138

• TN

  In order to comprehensively investigate the genetic relationship between PTC tumors and benign nodules, we totally collected 127 fresh-frozen biopsies samples from 28 patients with concurrent thyroid benign nodule and PTC (n=20) or simple benign nodule (n=8). We carried out whole-exome sequencing on all the 127 biopsies samples and RNA-sequencing in total of 40 samples.

  Dataset EGAD00001003351

• Dataset for neuroendocrine_adrenal_tumor-RNA

  Rare cancer sequencing data of 145 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008862

• The cellular immune and airway epithelial profile throughout childhood and in response to COVID-19 at multi-omic single cell level.

  Single-cell data gene expression data set (5’Chromium 10X) of healthy paediatric volunteers, and paediatric and adult COVID-19 patients. Gene expression was determined from samples of nasal, tracheal and bronchial brushings and blood (PBMCs). In addition to gene expression, PBMC’s were assayed by CITE-seq. A subset of samples have VDJ sequencing data for T cell receptors (TCR) and B cell receptors (BCR).

  Dataset EGAD00001007718

• The Institute of Cancer Research - Endocrinology Team

  Dac EGAC00001000532

• The Ashkenazi Genome Consortium Data Access Committee

  Dac EGAC00001000151

• The EMC-ILC3 consortium Data Access Committee

  Dac EGAC00001000729

• The Xiaoping Miao's lab of HUST.

  Dac EGAC00001000897

• Lead investigator of the TONIC study

  Dac EGAC00001001150

• The Jerusalem Perinatal Study (JPS) data access committee

  Dac EGAC00001001421

• Head of the circulating cells platform

  Dac EGAC00001001508

• Cancer Genomics of the Kidney - Targeted Sequencing

  Dac EGAC00001003091

• Spatial Dynamics of the Developing Human Heart

  Dac EGAC50000000616

• Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis

  Targeted therapy interventions using tyrosine kinase inhibitors (TKIs) provide encouraging treatment responses in ALK-rearranged lung adenocarcinomas, yet resistances occur almost inevitably. Apart from tumor cell-intrinsic resistance mechanisms, accumulating evidence supports a role of cancer-associated fibroblasts (CAFs) in affecting the therapeutic vulnerability of lung cancer cells. Here, we aimed to investigate underlying molecular networks shaping the therapeutic susceptibility of ALK-driven lung adenocarcinoma cells via tumor microenvironmental cues using three-dimensional (3D) spheroid co-culture settings. We show that CAFs promote therapy resistance of lung tumor cells against ALK inhibition by reducing apoptotic cell death and increasing cell proliferation. Using single-cell RNA-sequencing analysis, we show that genes involved in lipogenesis constitute the major transcriptional difference between TKI-treated homo- and heterotypic lung tumor spheroids. CAF-conditioned medium and CAF-secreted factors HGF and NRG1 were both able to promote resistance of 3D-cultured ALK-rearranged lung tumor cells via AKT signaling, which was accompanied by enhanced de novo lipogenesis and supression of lipid peroxidation. Notably, simultaneous targeting of ALK and SREBP-1 was able to overcome the established CAF-driven lipid metabolic-supportive niche of TKI-resistant lung tumor spheroids. Our findings highlight a crucial role of CAFs in mediating ALK-TKI resistance via lipid metabolic reprogramming and suggest new ways to overcome resistance towards molecular directed drugs by targeting vulnerabilities downstream of oncogenic signaling.

  Study EGAS50000000135

• To reveal the spectrum of gene mutations in grade II/III gliomas, whole exome sequencing of 52 samples including 4 multi-regional and 10 multi-time points sampling cases and 291 SNP-array were performed.

  To reveal the spectrum of gene mutations in grade II/III gliomas, whole exome sequencing of 52 samples including 4 multi-regional and 10 multi-time points sampling cases and 291 SNP-array were performed. Our analysis revealed high degrees of temporal/spatial heterogeneity generated during tumor expansion and relapse.

  Study EGAS00001001044

• Single-cell Transcriptomic and TCR Repertoire Profiling of DENV-specific CD8+ T Cells Across Dengue Disease Severities

  This dataset contains single-cell RNA sequencing (Smart-seq2) and paired TCR repertoire data of sorted dengue virus (DENV)-specific CD8⁺ T cells from individuals with differing clinical outcomes: asymptomatic dengue (AD), dengue fever (DF), and dengue hemorrhagic fever (DHF). Samples were obtained from HLA-A11⁺ and HLA-A24⁺ individuals during acute and convalescent phases, with antigen-specific CD8⁺ T cells isolated using HLA tetramers loaded with immunodominant DENV epitopes. The study identifies phenotypically distinct T cell subsets associated with disease severity, TCR avidity, and antigen reactivity to current or prior DENV serotypes. The dataset supports the understanding of CD8⁺ T cell heterogeneity, TCR features, and potential mechanisms of CD8⁺ T cell-mediated protection versus immunopathogenesis in dengue infection.

  Dataset EGAD00001015637

• Genome and transcriptome sequence data from an adenocarcinoma of the lung patient

  Genome and transcriptome sequence data from an adenocarcinoma of the lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003742

• Longitudinal Immune Dynamics of Mild COVID-19 Define Signatures of Recovery and Persistence

  SARS-CoV-2 has infected over 160 million and caused more than 3 million deaths to date. Most individuals (>80%) have mild symptoms and recover in the outpatient setting, but detailed studies of immune responses have focused primarily on moderate to severe COVID-19. We deeply profiled the longitudinal immune response in individuals with mild COVID beginning with early time points post-infection (1-15 days) and proceeding through convalescence to >100 days after symptom onset. We correlated data from single cell analyses of peripheral blood cells, serum proteomics, virus-specific cellular and humoral immune responses, and clinical metadata. Acute infection was characterized by vigorous coordinated innate and adaptive activation, including an early cellular and proteomic signature that correlated with the amplitude of virus-specific humoral responses after day 30. We characterized signals associated with recovery and convalescence to define a new signature of inflammatory cytokines, gene expression, and chromatin accessibility that persists in individuals with post-acute sequelae of SARS-CoV-2 infection (PASC).

  Study phs002576

• Genomic Copy-Number Variants Drive Apoptotic Resistance and Relapses on Immune Checkpoint Inhibitors

  We investigated the genomic mechanisms underlying acquired resistance (AR) to immune checkpoint inhibitors (ICIs) across tumor types, specifically by examining how copy number variant (CNV)-driven subclonal evolution contributes to clinical relapses in melanoma patients. We analyzed longitudinal clinical melanoma samples from patients who experienced relapses on ICI therapy, complemented by isogenic human melanoma cell line models (M486) and murine melanoma tumor systems. Single-cell whole-genome sequencing (scWGS) was employed to resolve subclonal CNV patterns in AR tumors. The scWGS data revealed that AR-dominant subclones systematically deleted pro-apoptotic genes while amplifying anti-apoptotic genes and innate resistance pathway components. Notably, shared and private AR subclonal CNVs preexisted selective pressure, with convergent evolution targeting apoptosis-regulatory pathways and resulting in downregulated apoptotic/mitochondrial priming that enables ICI resistance. scWGS datasets from isogenic human melanoma cell lines, patient-matched tumor samples, and murine melanoma models will be made available through dbGaP, enabling researchers to access high-resolution subclonal CNV profiles that define the genomic landscape of acquired ICI resistance evolution.

  Study phs004102

• Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures (Hipo_021)

  Cancer genomes harbor a broad spectrum of structural variants (SV) driving tumorigenesis, a relevant subset of which escape discovery using short-read sequencing. We employed Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post- therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assemble complex rearrangements and such associated with telomeric sequences, including a 1.55 Megabasepair chromothripsis event. We uncover a complex SV pattern termed ‘templated insertion thread’ (TI thread), characterized by short (mostly <1kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50kbp in size. TI threads occur in 3% of cancers, with a prevalence ranging to 74% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in cancer-driver genes. Our study shows the advantage of long-read sequencing in the discovery and characterization of complex somatic rearrangements.

  Study EGAS00001006629

• THE SAHEL 2.5 MILLION SNP ARRAY

  Dac EGAC00001000427

• The NOWAC study Data Access Committee

  Dac EGAC00001000521

• The Sample and Data Access Committee (SDAC) of CARTaGENE

  Dac EGAC00001000525

• The Ovarian Cancer Association Consortium Data Access Committee

  Dac EGAC00001000616

• The Kibbutzim Family study (KFS) data access committee

  Dac EGAC00001000805

• Genomic Heterogeneity and the Small Renal Mass

  Dac EGAC00001000875

• Present-day genomics from the Eurasian steppe

  Dac EGAC00001000878

• Genome Dynamics in the Immune system lab-imagine

  Dac EGAC00001001254

• DAC the Tel-Aviv Medical Center Neurosurgery dept

  Dac EGAC00001002176

• DAC Genetic variability in the glucocorticoid receptor NR3C1

  Dac EGAC00001002382

• The Solomon Islands: Human Origins array genotype data

  Dac EGAC00001002588

• The Ernest and Helen Scott Haematological Research Institute

  Dac EGAC00001002616

• The Swedish Childhood Tumor Biobank DAC

  Dac EGAC50000000095

• Hi-C on the OCIAML-2 Cell Line

  Study EGAS00001004743

• Age_Validation

  Rounded chronological age of the participants

  Dataset EGAD00010002753

• Age_TrainTest

  Rounded chronological age of the participants

  Dataset EGAD00010002755

• High coverage target resequencing of coding and regulatory regions of 38 Parkinson disease genes associated either to the Mendelian or the sporadic forms of the disease

  Coding sequences and putative regulatory sequences (retrieved from Ensembl and including up to 2500 bp of promoter sequence upstream the transcription start site) were re-sequenced to a mean depth of 49X on 38 genes associated to Parkinson's disease (RAB25, NUCKS1, RAB7L1, GBA, SYT11, ACMSD, STK39, MCCC1, STBD1, GAK, DGKQ, BST1, SCARB2, HLA-DRB5, GPNMB, FGF20, ITGA8, HIP1R, STX1B, SETD1A, SREBF1, MED13, RAI1, MAPT, RIT2, GIGYF2, HTRA2, EIF4G1, SNCA, LRRK2, VPS35, PINK1, DJ1, ATP13A2, UCHL1, PARK2, FBXO7, and PLA2G6). Sequencing was performed on 249 Parkinson's idiopathic cases and 145 unrelated controls of Spanish origin. All sequencing data was generated with an Illumina Hiseq2000 instrument after enrichment with a custom NimbleGen array. Raw reads were mapped to human reference genome hg19/GRCh37 using BWA aligner.

  Study EGAS00001000973

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established three kinds of esophageal tumoroids derived from esophageal cancer patient. We performed whole exome sequencing to analyze genetic background of the tumoroids.

  Study JGAS000749

• APC-related multiple salivary gland lesions

  This study aims to investigate the genetic and molecular mechanisms underlying a novel phenotype of attenuated familial adenomatous polyposis (AFAP), where affected individuals develop multiple salivary gland tumours, including basal cell adenomas and adenocarcinomas.

  Study EGAS50000001159

• Comprehensive analysis of interaction between human gene expression and environmental metagenomes.

  WGS, 10x scRNA, 10X TCR, 10X BCR and CyTOF analyses were performed using blood samples collected from healthy volunteers aged 18 years or older who worked or lived in the Kashiwa-no-ha area.

  Study JGAS000321

• Single cell sequences in patients with malignant tumors

  We perfomed single cell RNA and TCR sequencing of 2 lung adenocarcinoma patients and 3 head and neck squamous cell carcinoma to assess the detailed biological mechanisms of resistance to immune checkpoint inhibitors.

  Study JGAS000480

• Novel genome editing strategies to uncover genotype-phenotype correlations in Polycystic Kidney Disease: a proof-of-concept

  Bulk RNA-seq of genome-edited HEK293T cell lines engineered to model specific PKD1 variants. This dataset enables the exploration of genotype-phenotype correlations in Polycystic Kidney Disease (PKD)

  Study EGAS50000001188

• Molecular analysis of cancer genomes in children with Lynch syndrome: exploring causal associations

  Molecular characterization of 20 tumors of 18 children with Lynch syndrome to investigate causality. This characterization includes the investigation of second hits, tumor mutational load, mutational signatures and MMR protein expression.

  Study EGAS00001006992

• GEOCODE Cohort

  We built a large cohort of 406 healthy individuals and expanded the immune cis-regulome through their whole blood transcriptome obtained after stimulation with specific toll-like receptor (TLR) agonists and T-cell receptor (TCR) antagonist

  Study EGAS50000000903

• Breast_Cancer_Matched_Pair_Cell_Line_Whole_Genomes

  We propose to definitively characterise the somatic genetics of matched pair breast cancer cell lines through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000166

• Dopaminergic neuron differentiation of human embryonic stem cells

  2 replicates of dopaminergic neuron differentiation of human embryonic stem cells from timepoints day 17 and day 28, performed with 10X Genomics single cell RNA-seq. Part of the Ásgrimsdottir et al. (Arenas Lab).

  Study EGAS50000001099

• Triple_Negative_Breast_Cancer_Whole_Genomes

  We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000092