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• Mycobacterium_Induced_Granuloma

  Spatial transcriptomics of human Mycobacterium granulomas reveals Spatial and Functional Architecture of Immune Response and Tissue Remodeling

  Study EGAS50000000998

• Co-infection of fungi and bacteria in brain tissue of Alzheimer’s patients.

  Metagenomics analysis reveals co-infection of fungi and bacteria isolated from different regions of brain tissue from elderly persons and patients with Alzheimer's disease.

  Study EGAS00001002766

• Exome and transcriptome sequencing of Desmoplastic Small Round Cell Sarcoma

  To conduct exome and transcriptome profiling to identify secondary recurrent mutations, multi-site phylogenetic analyse and immune characterization of Desmoplastic Small Round Cell Sarcoma.

  Study EGAS00001004575

• Gene_epression_regulation_in_cytokine_induced_immune_cell_states

  We isolated T cells and monocotyes from healthy platelet donors and cultured them in resting and stimulated conditions with addition of a range of cytokines. We performed RNA sequencing to assess impact of different disease-relevant cytokines upon immune cell responses.

  Study EGAS00001003823

• HLF COPD Transcriptomics

  We generated transcriptomes of primary human lung fibroblasts (HLFs) isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease. RNA sequencing analysis demonstrated dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization.

  Study EGAS00001006602

• Genomic and transcriptomic landscape of aggressive thyroid cancer

  Molecular characteristics of anaplastic thyroid cancer (ATC) and advanced differentiated thyroid cancers (DTCs) have not been fully elucidated. In this study, we applied various types of massively-parallel sequencing technology to 113 advanced TCs, including 27 ATCs and 86 advanced DTCs, to reveal their genomic and transcriptomic characteristics.

  Study EGAS00001003540

• Evaluation of capture and amplicon-based targeted sequencing methods on formalin-fixed tumours

  Evaluated performance of three capture (Agilent’s SureSelectXT HS, Illumina’s Nextera Rapid Capture Custom, and New England Biolabs’ Next Direct Custom) and one amplicon-based (Qiagen’s Human Breast Cancer Panel) targeted sequencing methods on paired blood and FFPE, using whole exome sequencing data from matched fresh-frozen tissue as a comparison.

  Study EGAS00001004965

• Novel Gene-Environment Regulatory Circuit in Chamber-Specific Growth of Perinatal Heart

  We report a case of hypertrophic cardiomyopathy and lactic acidosis in a 3-year-old female. Cardiac and skeletal muscle biopsies exhibited mitochondrial hyperplasia with decreased complex VI activity. Whole exome sequencing identified compound heterozygous variants, p.Arg333Trp and p.Val119Leu, in TSFM, a nuclear gene that encodes a mitochondrial translation elongation factor, resulting in impaired oxidative phosphorylation and juvenile hypertrophic cardiomyopathy.

  Study phs002725

• A Phase II Study: CRS207/GVAX Plus Anti-PD1 and Anti-CTLA4 Recruits Mesothelin- and KRAS-Specific T cells into PDAC

  This study examined immunologic correlatives from a phase II study evaluating CRS207/GVAX vaccines in combination with anti-PD1 and anti-CTLA4 in metastatic pancreatic cancer (NCT03190265). Arm A received CRS207/GVAX with anti-PD1 and anti-CTLA4 therapy; Arm B received CRS207 with anti-PD1 and anti-CTLA4 therapy. Patients undergoing treatment in this trial had peripheral blood mononuclear cells (PBMCs) and tumor tissue biopsied serially at pre-treatment and on-treatment timepoints. Single-cell RNA/TCR sequencing was employed on PBMCs. Bulk RNA/TCR sequencing was employed on tumor tissues. We identified treatment-enriched inflammatory pathways as well as T cell repertoires.

  Study phs003798

• NOTCH1 orchestrates metabolic reprogramming to drive proliferation in chronic lymphocytic leukemia

  In Chronic lymphocytic leukemia (CLL), NOTCH1 mutations occur in ~10% of cases and are often associated with unmutated IGHV genes, defining a subgroup requiring earlier treatment. Using an engineered CLL cell line, we demonstrated that NOTCH1-mutated cells exhibit increased glucose uptake, oxidative metabolism, and proliferation, driven by enhanced mitochondrial mass and TFAM upregulation. Metabolic assays and stable isotope tracing revealed a greater dependency on glutamine and anabolic pathways in NOTCH1-mutated cells, promoting growth. These findings were validated in a cohort of NOTCH1-mutated patients, highlighting a molecular circuit linking BCR, NOTCH1, and mitochondrial metabolism. This study suggests that metabolic vulnerabilities in NOTCH1-mutated CLL could inform precision medicine strategies.

  Study EGAS50000000981

• Single cell RNA sequencing of synovial B cells in early Rheumatoid Arthritis

  This dataset includes 3432 paired single cell sequencing fastq files derived from synovial B cells of 5 early Rheumatoid Arthritis patients. Libraries were prepared using the SmartSeq2 protocol. All wells contained ERCC spike-ins. Libraries were sequenced on an Illumina NovaSeq instrument with 2x100bp paired-end reads yielding a median of 2.5M reads/well. Sample aliases ending on 368 and 384 represent empty control wells. Sample aliases starting with P11417_4 and P13157_1 belong to ACPA- patient A7, sample aliases starting with P11417_5 and P11417_6 belong to ACPA+ patient A1, sample aliases starting with P13157_2 belong to ACPA- patient A3, sample aliases starting with P13157_3 and P13157_6 belong to ACPA+ patient A2, sample aliases starting with P13157_4 and P13157_5 belong to ACPA- patient A4.

  Dataset EGAD00001009076

• Whole genome sequencing analysis of hepatoblastoma

  Whole genome sequencing analysis of pediatiric liver tumor, hepatoblastoma, and their genomic and epigenomic features.

  Study JGAS000156

• Duplex Sequencing of normal and tumor tissues from case 2 and case 3 (10 DS)

  Duplex Sequencing of normal and tumor tissues from case 2 and case 3 (10 DS)

  Dataset EGAD50000000239

• Genomics_of_Colorectal_Cancer_Metastases___Massively_Parallel_Sequencing_of_Matched_Primary_and_Metastatic_tumours_to_Identify_a_Metastatic_Signature_of_Somatic_Mutations__MOSAIC_

  Exome pulldown and SNP6 Affymetrix array of matched primary and metastatic colorectal cancer samples from 20 patients

  Study EGAS00001000103

• Organoid_Derivation_Project__TGS

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients.

  Study EGAS00001002221

• FWO_project_G_0687_12_X10_WGS

  Profiling subclonal architecture and phylogeny in tumors by whole-genome sequence data mining and single-cell genome sequencing

  Study EGAS00001001145

• Whole exome sequencing of PMBCL

  Whole exome sequencing of 8 PMBCL samples and paired normal samples and 14 unpaired PMCL samples.

  Study EGAS00001006235

• RNA sequencing of Non-Small Cell Lung Cancer and adjacent normal tissue

  RNA sequencing was performed on 108 NSCLC tumor samples and their paired adjacent normal tissues (n=21) to identify associations with clinical and immune characteristics.

  Study EGAS50000000246

• Genomic WES plasma control samples

  This datasets consists os genomic WES of paired-end raw data (FASTQ R1, R2 and UMI sequence) obtained from plasma and HapMap control samples. Specifically, it consists in two Hapmap samples (NA12877, NA12878) and 2 plasma standarts (HD780 and HD816) with VAF mutations at 0.0%, 0.1%, 1.0%, and 5.0%, in total 21 plasma samples.

  Dataset EGAD50000000805

• single cell data from HPV-positive head and neck cancer patients receiving induction CTLA-4 and PD-1 immune checkpoint blockade

  Baseline and on-treatment tumor samples from human papillomavirus-positive oropharynx cancer patients receiving anti-CTLA-4 and anti-PD-1 immune checkpoint blockade were analyzed by single-cell RNA and TCR sequencing.

  Dataset EGAD50000000487

• Whole-genome DNA methylation profiling of CD14+ monocytes reveals disease status and activity differences in Crohn’s disease patients

  Identifying differences in CD14+ monocyte methylation between CD and non-CD patients, as well as between CD-active and CD-remissive patients.

  Study EGAS00001004221

• Transcriptome sequencing of fibroblast-dependent alveolar organoids derived from patient-specific iPS cells with SFTPC^Y104H variant and their gene-corrected (monoallelic wild type SFTPC) ones.

  A disease-specific iPS cell line derived from a pulmonary fibrosis patient with SFTPC^Y104H and its gene-corrected (monoallelic wild type SFTPC) one were established. Then lung progenitor cells were differentiated from each cell line and co-cultured with human fetal lung fibroblasts to generate alveolar organoids, respectively. Alveolar epithelial cells and fibroblasts were isolated by fluorescence-activated cell sorting and each RNA was extracted. We performed transcriptome analysis of those samples by RNA-sequencing.

  Study JGAS000617

• Convergent genetic adaptation in human tumors developed under systemic hypoxia and in populations living at high altitudes

  Genomic files, including whole-exome and RNA-seq data from tumors and cell lines, were generated and analyzed in this study.

  Dac EGAC50000000484

• PE-META-EUROPE_CENTRAL_ASIA-MATERNAL

  Fixed effect meta-analysis summary statistics combining GWAS of maternal preeclampsia cases and controls from Europe (UK, Iceland, Norway, Denmark and Finland) and Central Asia (Kazakhstan and Uzbekistan).

  Dataset EGAD00010001988

• PE-META-EUROPE_CENTRAL_ASIA-FETAL

  Fixed effect meta-analysis summary statistics combining GWAS of fetal (baby) preeclampsia cases and controls from Europe (UK, Iceland, Norway, and Denmark) and Central Asia (Kazakhstan and Uzbekistan).

  Dataset EGAD00010001983