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• Single cell RNA sequencing of bone marrow mononuclear cells from healthy donors and B-cell lymphoma patients following CD19 CAR T-cell therapy

  Bone marrow aspirates were obtained from patients with relapsed/refractory large B cell lymphoma (rrLBCL), mononuclear cells isolated by ficoll density-gradient centrifugation, and loaded onto a 10X Chromium for single cell RNA-sequencing using 5’ chemistry without prior cryopreservation. Healthy donor bone marrow mononuclear cells were obtained from healthy allogeneic stem cell transplant donors and analyzed following viable cryopreservation.

  Dataset EGAD00001009774

• Whole Exome and RNA-Sequencing of Germline, Small Bowel Carcinoid Primary Tumor, and Liver Metastasis Trios

  This dataset includes trios of germline/constitutional, primary tumor (small bowel carcinoid), and metastatic tumor (liver) trios for 5 patients (i.e. 15 samples total). Constitutional, primary tumor, and metastatic tumor samples all underwent whole exome sequencing (WES or WXS). Primary and metastatic tumor samples underwent RNA sequencing (RNA-seq).

  Dataset EGAD00001010036

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0188_002A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0188_002A for Diffuse large B-cell lymphoma patient sample TFRIPAIR11_DLBCL

  Dataset EGAD00001010234

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0197_002A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0197_002A for Diffuse large B-cell lymphoma patient sample TFRIPAIR12_DLBCL_rel

  Dataset EGAD00001010235

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0198_002A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_002A for Diffuse large B-cell lymphoma patient sample TFRI_Pair_13_DLBCL

  Dataset EGAD00001010236

• HiChIP bulk

  This dataset gather HiChIP data for H3K27ac mar in MM.1S cell line in control and Dex condition, both in two biological replicates

  Dataset EGAD00001011138

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0079_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0079_001 for Triple negative breast cancer sample SA1035X6XB03216

  Dataset EGAD00001011241

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0079_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0079_002 for Triple negative breast cancer patient-derived xenograft SA1035X6XB03211

  Dataset EGAD00001011242

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0145_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0145_001 for Triple negative breast cancer patient-derived xenograft SA1035X7XB03338

  Dataset EGAD00001011244

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0145_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0145_002 for Triple negative breast cancer patient-derived xenograft SA1035X7XB03340

  Dataset EGAD00001011245

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0151_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0151_001 for Triple negative breast cancer patient-derived xenograft SA1035X8XB03425

  Dataset EGAD00001011247

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0175_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0175_002 for Triple negative breast cancer patient-derived xenograft SA1035X8XB03631

  Dataset EGAD00001011249

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0014_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0014_001 for Triple negative breast cancer patient-derived xenograft SA604X6XB01979

  Dataset EGAD00001011251

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0015_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0015_001 for Triple negative breast cancer patient-derived xenograft SA604X6XB01979

  Dataset EGAD00001011252

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0019_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0019_001 for Triple negative breast cancer patient-derived xenograft SA604X7XB02089

  Dataset EGAD00001011253

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0020_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0020_002 for Triple negative breast cancer patient-derived xenograft SA604X8XB02164

  Dataset EGAD00001011254

• 10x Single Cell Gene Expression Library TENX063

  10x Single Cell Gene Expression library TENX063 for Triple negative breast cancer patient-derived xenograft SA609X3XB01584

  Dataset EGAD00001011268

• Whole genome sequencing of tumor samples from advanced pre-treated NSCLC patients recruited in a phase I/II single-arm trial utilising CVA21, an oncolytic coxsackie virus, in combination with pembrolizumab.

  This dataset contains paired tumor and matched normal whole-genome sequencing (WGS) data from longitudinally collected samples of patients enrolled in an Australian clinical study involving multiple cancer types. For each patient, one or more tumor biopsies were obtained at different treatment time points (Scr, Day 0, Day 15, Day 22, Day 33), and matched normal samples were collected either from blood or non-tumor tissue.

  Dataset EGAD00001015682

• Investigation of 3D chromatin structure in clear cell renal cell carcinoma

  In order to investigation the 3D chromatin structure in clear cell renal cell carcinoma (ccRCC), we performed ultra high-resolution chromatin capture using MNase (Micro-C) in 786-O, A-498, UM-RC-2 ccRCC cell lines, as well as HK-2 normal renal epithelium cell line, cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. Data are provided in raw fastq and the chromatin interactions in hic format. Data were processed using the Juicer pipeline.

  Dataset EGAD50000001884

• 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

• Biallelic HMBS Inactivation Defines a Homogenous Clinico-Molecular Subtype of Hepatocellular Carcinoma

  Acute intermittent porphyria (AIP), caused by heterozygous germline mutations of the heme synthesis pathway enzyme HMBS (hydroxymethylbilane synthase), confers high risk of hepatocellular carcinoma (HCC) development. Yet, the role of HMBS in liver tumorigenesis remains unclear. Here we explore HMBS alterations in a large series of 758 HCC. We identify recurrent bi-allelic HMBS inactivation, both in AIP patients acquiring a second somatic HMBS mutation and in sporadic HCC with two somatic hits. HMBS alterations are enriched in truncative mutations, in particular in splice regions, leading to abnormal transcript structures. Bi-allelic HMBS inactivation results in a massive accumulation of its toxic substrate porphobilinogen and synergizes with CTNNB1 activating mutations, leading to the development of well differentiated tumors with a transcriptomic signature of Wnt/ß-catenin pathway activation and a DNA methylation signature related to ageing. HMBS-inactivated HCC mostly affect females, in absence of fibrosis and classical HCC risk factors. These data identify HMBS as a tumor suppressor gene whose bi-allelic inactivation defines a homogenous clinical and molecular HCC subtype.

  Study EGAS00001005986

• 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

• 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).

  Study EGAS50000000342

• A108846B

  Whole genome sequencing for single cells for library A108846B 1636 cells; filetype=bam

  Dataset EGAD00001007092