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• Synchronous patterning of hiPSC-derived CNS progenitors generates comprehensive axial spinal cord organoids (CASCOs) containing diverse motor neuron population

  Advancements in human induced pluripotent stem cell (hiPSC) culture have enabled the generation of spinal cord organoids (SCOs), though achieving distinct axial identities in spinal motor neurons (spMNs) along the rostro-caudal (RC) axis remains a challenge. By optimizing the timing and sequence of patterning factors, we developed a mixed stem cell model of rostral neural stem cells (NSCs) and caudal neuromesodermal progenitors (NMPs) to generate SCOs with enhanced spMN heterogeneity, including a wide range of axial identities and benchmarked this against commonly used protocols. Our approach, termed CASO (Comprehensive Axial Spinal Organoids), also incorporates endothelial networks and skeletal muscle to improve organoid complexity and health, offering a novel method to study spMN axial specification and model neurodegenerative diseases.

  Study EGAS50000000891

• Clinical Outcomes of 344 Diffuse Large B-Cell Lymphoma patients

  This study examines clinical outcomes of patients with diffuse large B-cell lymphoma (DLBCL). We analyzed a cohort of 344 patients from the German High-Grade Non-Hodgkin Lymphoma Study Group (DSHNHL). To protect patient confidentiality, all samples were pseudonymized. The dataset includes clinical key characteristics, such as patient age at diagnosis, sex, ECOG performance status, disease stage, serum lactate dehydrogenase levels, bulky disease, bone marrow involvement, extranodal involvement, and B-symptoms. We used these data alongside proteomic and transcriptomic profiles to explore relationships between clinical features and molecular signatures, reconstructing regulatory networks. Insights from this integrative analysis aim to identify key pathological drivers and biomarkers of DLBCL progression, ultimately informing improved risk stratification and targeted therapeutic approaches.

  Study EGAS50000001054

• 1. Identidication of molecular biological mechanism associated with the development and prognosis of uterine cancer, uterine sarcoma, and endometrial hyperplasia / 2. Identification of molecular biological mechanism associated with the development of endometriosis and malignant transformation, ovarian cancer, fallopian tubal cancer, peritoneal cancer, and other malignant tumors in gynecological organs

  To clarify the biological difference between clear cell carcinoma and other histological subtypes in ovarian carcinomas by comparing copy number variants, and to identify molecular subtypes and carcinogenesis in clear cell ovarian carcinomas by whole-exome sequencing and RNA-sequencing. Then, characterize high-grade serous carcinomas by NGS-based, integrative genomic analyses, with focus on homologous recombination deficiency, molecular subtypes, prognostic factors and effectiveness of PARP inhibitor. Based on the results of whole-exome sequencing, an investigator-initiated, phase 2 clinical trial will be conducted to evaluate the efficacy and safety of the PARP inhibitor olaparib in HRD-positive cases.

  Study JGAS000789

• Investigating the differences in iPSC-derived intestinal epithelial cell behaviour and composition grown as organoid, in Transwell or Intestine-Chip.

  aim: Investigating the differences in iPSC-derived intestinal epithelial cell behaviour and composition grown as organoid, in Transwell or Intestine-Chip. RNA sequencing data of 21 samples of iPSC-derived intestinal epithelial cells on different model systems. 3 iPSC lines Geni002, Geni007 and Geni012 differentiated into Epcam+ intestinal epithelial cells and grown on the following systems: 6 samples: organoids exposed to EM (3) and DM+D+PD (3) 9 samples: Transwell exposed to EM/EM (3), DM+D+PD/DM+D+PD (3), EM/DM+D+PD (gradient, 3) 6 samples: Emulate Chip exposed to EM/EM (3) and EM/DM+D+PD (3) EM: expansion medium DM+D+PD: differentiation medium including DAPT and PD0325901

  Study EGAS50000001339

• RNAseq data of polyA+ RNA from Leukocytes from 624 individuals of the SardiNIA cohort.

  We sequenced the polyA+ of the RNA of the leukocytes from 624 sardinian individuals with RNAseq (Illumina 2000, an average of round 60M reads per sample, 51 + 51 nt). Combining the genotype information of the same individuals (already available from the ProgeNIA project) with the transcriptome data we identified 21,183 independent expression quantitative trait loci (eQTLs) and 6,768 independent splicing quantitative trait loci (sQTLs), including 619 novel QTLs that exhibit population-specific trait associations. Using family relationships, we identified 809 segregating expression outliers and provide a new approach to study large effect regulatory variants and their relevance to traits. Our results provide insight into the effects of regulatory variants and their relationship to population history and individual genetic risk.

  Study EGAS00001002105

• Understanding_the_multicellular_dynamics_of_clear_cell_renal_cell_carcinoma___DNA_sequencing

  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 EGAS00001003517

• Whole Exome Sequencing in Multiple Myeloma

  By whole exome sequencing (WES) our group observed the accumulation of mutations in receptor tyrosine kinases (RTKs), adhesion molecules and their effectors and developed a signaling network that was affected by at least one mutation in almost 100% of MM patients and by more than one mutation in around 50% of MM patients which we decided to call inter- and intra-individual pathway redundancy. Interestingly, the extension of our WES dataset to 67 primary MM samples with correspond normal tissue which were collected at the Medizinische Klinik and Poliklinik II in Würzburg within the frame of the CRU216 has tentatively led to the designation of three molecular subgroups based on their mutation profile: "adhesion only", "adhesion & downstream" and "RTK & adhesion & downstream

  Study EGAS00001003227

• Understanding_the_multicellular_dynamics_of_clear_cell_renal_cell_carcinoma___single_cell_RNA_sequencing

  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 EGAS00001003519

• Neuroblastoma tumor heterogeneity and cell plasticity (from patients)

  Two cell identities, noradrenergic and mesenchymal, have been characterized in neuroblastoma cell lines according to their epigenetic landscapes relying on specific core regulatory circuitries of transcription factors. Yet, their relationship and relative contribution in patient tumors remain to be defined. Here, we document a spontaneous plasticity between the noradrenergic and mesenchymal identities in a subset of cell lines. Strikingly, mesenchymal neuroblastoma cells revert to a noradrenergic phenotype in vivo. Consistently, tumor cells with a mesenchymal identity are detected in single-cell transcriptomic analyses of neuroblastoma tumors and PDX models. Our data also highlight neuroblastoma intra-tumor heterogeneity with the co-existence of distinct tumor populations, including sympathoblast-like and chromaffin-like cells suggesting that neuroblastoma cells arise from a common sympatho-adrenal progenitor.

  Study EGAS00001005322

• Comparison between phenotypic-defined stage of blasts and transcriptional profile

  Established a proof-of-concept methodology with potential integration into flow cytometry software for objective AML subtype classification based on blast differentiation, offering valuable prognostic insights for elderly patients.

  Study EGAS50000000336

• Dataset for other_cancer-RNA

  Rare cancer sequencing data of 95 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008847

• Southern African Prostate Cancer Study (SAPCS) Ethnic Disparity

  The cohort (n=130) consists of prostate cancer patients from South Africa (n=123) and Brazil (n=7). For each patient, a pair of blood and tumour samples were collected. The sequencing data was mapped to hg38 reference. Blood BAMs are named with “-B” as suffix and tumour BAMs are named with “-T” as suffix.

  Dataset EGAD00001009067

• Identification of colorectal cancer susceptibility genes in Japanese

  We performed whole genome sequencing of 617 colorectal cancer patients registered in BioBank Japan to identify novel susceptibility genes.

  Study JGAS000699

• Whole-exome-sequencing in Frontotemporal dementia (FTD)

  To identify the genetic cause and modifiers of Frontotemporal dementia (FTD), we performed Whole-exome-sequencing of FTD patients.

  Study JGAS000374

• Identification of gastric cancer susceptibility genes in Japanese

  We performed whole genome sequencing of 256 gastric cancer patients registered in BioBank Japan to identify novel susceptibility genes.

  Study JGAS000698

• Identification of gastric cancer susceptibility genes in Japanese

  We performed whole genome sequencing of 2067 gastric cancer patients registered in BioBank Japan to identify novel susceptibility genes.

  Study JGAS000701

• Identification of diabetes mellitus susceptibility genes in Japanese

  We performed whole genome sequencing of 2162 diabetes mellitus patients registered in BioBank Japan to identify novel susceptibility genes.

  Study JGAS000700

• Whole exome sequencing of colorectal cancer

  To elucidate immune status of solid tumors including gastrointenstinal cancer, we performed whole exome sequencing of colorectal cancer 7 patients.

  Study JGAS000279

• BASIS_Genome_Validation_Study

  Bespoke validation experiments will be performed on ER+ Breast Cancer cases to confirm the presence of mutations found in whole genome sequencing.

  Study EGAS00001000403

• HCA_Gut_Paediatric_Hirschsprung_s_disease_Teichmann_Spatial_Managed_Access_

  This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease.

  Study EGAS00001007152

• ENCORE__New_Targets_for_Effective_Combination_Therapies_in_Tumors_with_Unmet_Medical_Need

  This study utilises 2G-CRISPR screens to identify effective target combinations in KRAS-mutant colorectal and triple-negative breast cancer cell lines.

  Study EGAS00001004775

• Evolutionary dynamics of neuroblastoma

  Whole genome sequencing data of low risk neuroblastoma tumors and matching controls used to study the evolutionary dynamics of neuroblastoma.

  Study EGAS00001004990

• The genomic landscape of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21

  Use scRNA-seq data from 4 iAMP21 patients to study the clonal evolution of iAMP21.

  Study EGAS00001006577

• HCA_Gut_Paediatric_Hirschsprung_s_disease_Teichmann_RNA_Managed_Access_

  This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease.

  Study EGAS00001007151

• HCA_Gut_Paediatric_Hirschsprung_s_disease_Teichmann_WGS_Managed_Access

  This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease.

  Study EGAS00001007437