Search Results - EGA European Genome-Phenome Archive

Thymic epithelial transplantation for complete DiGeorge syndrome Spatial (2026-01-19)

Spatial transcriptome analysis of thymic cells from children with syndromic diseases such as Trisomy 21 and inflammatory/autoimmune diseases such as myasthenia gravis. . This dataset contains all the data available for this study on 2026-01-19.

Dataset EGAD00001015798

Understanding the development of resident memory T cells (Trm) in the human small intestine using integrative multiomic approaches: Paediatric RNA (2026-01-15)

This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease. . This dataset contains all the data available for this study on 2026-01-15.

Dataset EGAD00001015797

DC Manuscript 2026

Dac EGAC50000000925

REL-2017-07-2026

HipSci - Hypertrophic Cardiomyopathy - Expression Array - July 2017

Dataset EGAD00010001380

Learning from the thymic human cell atlas for T cell engineering: Paediatric RNA (2025-10-02)

T cells are central to adaptive immunity and thus crucial for understanding and treating human disease. While extensively studied in model organisms, translating this knowledge to humans can sometimes be limited by their rapid cross-species evolution and diverse . This dataset contains all the data available for this study on 2026-03-10.

Dataset EGAD00001015720

WGS data of conditional knockout mouse model mammary tumours

Deposited here are 56 whole-genome sequencing BAM files from 15 Trp53f/w, 12 Trp53f/f, 14 Brca1f/f Trp53f/w, and 15 Brca1f/f Trp53f/f mouse mammary tumor samples sequenced on Illumina NovaSeq PE150. An additional 6 whole genome sequencing BAM files from corresponding normal tissues of mice are also included as controls (BPC_D666, B1PC_D840, BPTC_D992, PC_D503, PC_D720_Kid, PTC_H531). All samples were used in the study “Insights into BRCA1 and TP53 associated breast cancer development from integrated whole genome analysis of mouse model mammary tumors, Huo et al., 2026.”

Dataset EGAD50000002036

The EGA Helpdesk team: 2025 in review and what we are building next

Behind every dataset submitted, every access request processed, and every technical question answered, there is a team working quietly to keep things moving: the Helpdesk (HD). With the onset of 2026, this feels like the right moment to look back on what 2025 has been like for the HD team: the challenges we faced, how we adapted, and where we're heading next. Why the Helpdesk matters to EGA The EGA Helpdesk is more than a support channel. It plays a key role in maintaining trust in the EGA ecosystem. By supporting data submitters, researchers, Data Access Committees (DACs), and institutional partners, the HD helps ensure that data can flow securely, efficiently, and reliably. When issues arise, the Helpdesk is often the first place where their impact is felt and addressed. In that sense, the HD sits at the intersection of technology, policy, and people. One Helpdesk, two locations, one shared mission The EGA Helpdesk is a joint, distributed team working closely across two locations: CRG (Barcelona, Spain) and EMBL-EBI (Cambridge, UK). Although we are based in different institutions, we operate as a single Helpdesk, with shared workflows, priorities, and responsibility towards users. At CRG, the HD team is formed by: Andrea Max Àlex and me At EMBL-EBI, we work closely with: Silvia Coline Aravind What defines us as a team is simple: we work user-first, even under pressure. In a highly technical environment, clarity, empathy, and consistency matter just as much as tools and processes. A close collaboration across sites is essential to making that happen. What does the EGA Helpdesk do? The HD supports users across the full lifecycle of data in EGA. This includes: Data submissions, uploads, and encryption workflows. Data access requests and permissions. Questions around policies, consent, and data usage. Technical and system-related issues. Coordination between users, internal teams, and external partners. 2025: growth, change, and recalibration 2025 was a year of growth, but not always a predictable one. Early in the year, several technical and system-related challenges required us to adjust our original plans. Priorities shifted, timelines changed, and some improvements had to be rethought. For the HD team, this is often the hardest part of the job: we see delays through the eyes of users and understand the real impact they can have on ongoing research. One of the key lessons from 2025 was that stability is not only a technical challenge, but also an organisational one. Teamwork proved to be essential: anticipating peak periods, sharing context early, and coordinating closely across teams made a tangible difference. When things became complex, working together across roles and locations was what allowed us to keep moving forward. In 2025, the Helpdesk received 5.313 tickets and resolved 5.511 requests, reflecting both increased adoption of EGA and the team’s ability to absorb higher demand. At the same time, demand continued to grow. Compared to 2024, ticket creation increased by over 6%, while resolution capacity grew by more than 11%. The team not only kept up with incoming requests but also resolved part of the accumulated backlog, finishing the year having solved more tickets than were created. The real challenge of 2025 was not overall performance, but how the workload was concentrated during peak months. Seasonality and demand spikes placed pressure on the system, even while overall efficiency remained strong. On a team level, 2025 was also a year of transition. I joined the HD leadership role in January 2025, stepping into a period of change and rapid learning. Later in the year, in October, we said goodbye to Raül, and in January 2026, we welcomed Àlex, strengthening the team for the next phase. What users needed most in 2025 While requests vary widely, some themes stood out throughout the year: Support with data submissions and uploads Data access requests and permissions Technical and system-related issues As EGA matures, day-to-day operations have become more complex. Many long-running tickets are not delayed due to a lack of follow-up, but because they depend on external approvals, cross-institutional coordination, or multi-step processes. Understanding these patterns helps us focus not just on resolving tickets, but on improving how work flows through the system. Looking ahead to 2026 With a reinforced team and clearer insights from 2025, our focus for 2026 shifts from throughput to flow. Key priorities include: Strengthening our web content and documentation Reducing structural backlog Improving cross-team and cross-system coordination Anticipating peak demand earlier and planning capacity accordingly Challenges will continue to arise in 2026, as they always do. However, 2025 reinforced something important: a stable, empathetic, and well-aligned Helpdesk team is essential to supporting EGA's mission at scale. Supporting users well means supporting research, and that remains at the core of what we do.

Blog ega-helpdesk-team-2025-in-review-and-upcoming-improvements

Projects

Projects Jointly managed by the European Bioinformatics Institute (EMBL-EBI) in Cambridge (UK) and the Centre for Genomic Regulation (CRG) in Barcelona, the EGA provides an invaluable service to the worldwide biomedical research community. The teams leading the EGA are involved in several international partnerships and consortia in numerous scientific fields, where they contribute to ambitious projects. In addition to the project listed below, The EGA is in a long-standing partnership with the Global Alliance for Genomics and Health (GA4GH), as described on the dedicated page. On-going projects Project Duration Domain Funder Tags EASIGEN-DS | The EASIGEN-DS project aims to conduct a design study to establish a new European Research Infrastructure on Advanced Genomics Technologies, EASIGEN. To develop an excellent scientific, technological and operational design, we will conduct landscape studies, stakeholder consultations, and community surveying. 2025-2028 Genomic and health data Horizon Europe DATA MANAGEMENT DOCUMENTATION INFRASTRUCTURE Go-IMPaCT | Go-IMPaCT will contribute sequenced genomes and provide infrastructure as part of IMPaCT-Cohort, one of the three fundamental pillars of the Precision Medicine Infrastructure associated with Science and Technology (IMPaCT) program in Spain. Along with the Genome of Europe (GoE) project, around 18.000 people will have their genomes sequenced, also contributing to Spain's commitments in 1+MG. Go-IMPaCT will fund the development of an EGA node to manage and share this genomic and phenoclinic data, laying the foundations for regional and ethnic genomic variability in Spain to be available for research purposes. The IMPaCT cohort is created with the spirit of being an open research tool, compatible with the rest of the health research ecosystem, and other international initiatives. 2025-2027 Large-scale genomics and health data; personalised medicine Instituto de Salud Carlos III ACCESS DISCOVERY INFRASTRUCTURE METADATA STANDARDS FAIR-FEGA | This project seeks to accelerate data depositions into FEGA, significantly increasing the data flow in and from FEGA nodes. It will build capacity within the FEGA nodes and increase awareness in a wide range of stakeholders, thus altogether achieving the ultimate goal of enhancing data reuse. The project will be carried out by a strategic consortium comprising seven ELIXIR nodes and two ELIXIR communities. 2025-2026 Not applicable ELIXIR ACCESS DISCOVERY DOCUMENTATION INFRASTRUCTURE METADATA STANDARDS FEGA-Connect | A consortium of six ELIXIR nodes plus the Polish FEGA node (in-kind contribution) joining forces to build a solid base to develop solutions for effective multi-omic sensitive data integration between FEGA nodes and other infrastructures and specialised Data repositories. We aim to promote a more coherent data deposition, discoverability and retrieval of multi-omics datasets, providing FAIRer data and consequently accelerating research. 2025-2026 Multi-omics data ELIXIR ACCESS DATA MANAGEMENT DISCOVERY INFRASTRUCTURE METADATA STANDARDS IMPaCT-Data 2 | IMPaCT-Data 2 will develop a digital platform for the integration and modelling of biomedical data associated with IMPaCT (Precision Medicine Infrastructure associated with Science and Technology) projects in Spain. It will deploy a sustainable infrastructure that facilitates the integration, standardisation, interoperability and analysis of clinical, genomic, molecular and medical imaging data. This platform will be aligned with European projects such as Genome of Europe (GoE), the first project to make use of the European Genomic Data Infrastructure (GDI), and EUCAIM. IMPaCT-Data 2 will benefit from advanced Artificial Intelligence and High Computing Capacity Systems capabilities, offering robust and accessible tools for researchers from the National Health System in Spain. 2025-2026 Large-scale genomics and health data; personalised medicine Instituto de Salud Carlos III ACCESS DISCOVERY INFRASTRUCTURE METADATA STANDARDS ERDERA | The European Rare Disease Research Alliance (ERDERA) takes over EJPRD to deliver concrete health benefits to rare disease patients in the next decade by advancing prevention, diagnosis and treatment research. To leave no one behind, over 170 organisations championed by the European Union and member states are working hand in hand to make Europe a world leader in rare diseases research and innovation. 2024-2034 Rare diseases Horizon Europe; "La Caixa" Foundation cofunds CRG's contribution ACCESS DATA ANALYSIS DISCOVERY INFRASTRUCTURE GoE | The Genome of Europe initiative aims to build a European network of national genomic reference cohorts of at least 500.000 citizens. These reference cohorts will be selected to be representative of the European population. 2024-2028 Large-scale genomic and health data Horizon Europe ACCESS DISCOVERY INFRASTRUCTURE METADATA STANDARDS HEREDITARY | HEREDITARY aims to transform the way we approach disease detection, prepare treatment response, and explore medical knowledge by building a robust, interoperable, trustworthy, and secure framework that integrates multimodal health data (including genetic data) while ensuring compliance with cross-national privacy-preserving policies. 2024-2027 Neurodegenerative disorders, gut-brain interplay Horizon Europe DATA MANAGEMENT DATA ANALYSIS EOSC-ENTRUST | The mission of EOSC-ENTRUST is to create a European network of trusted research environments for sensitive data and to drive European interoperability by joint development of a common blueprint for federated data access and analysis. 2024-2026 Trusted Research Environment Horizon Europe INFRASTRUCTURE EBV-MS | "Targeting Epstein-Barr Virus Infection for Treatment and Prevention of Multiple Sclerosis". The ambitious goals of the project are to answer the questions why only a few EBV infected persons develop MS, and define the underlying mechanism of this process, as well as clarify if targeting the EBV infection can prevent MS or improve the disease course. 2023-2028 Viral-host genetics; immune response; disease modelling; Disease prevention Horizon Europe DATA MANAGEMENT DATA ANALYSIS WISDOM | WELL-BEING IMPROVEMENT THROUGH THE INTEGRATION OF HEALTHCARE AND RESEARCH DATA AND MODELS WITHOUT BORDER FOR CHRONIC IMMUNE-MEDIATED DISEASES aims to deploy novel approaches for data processing, harmonisation, management, and secure data sharing and federated access for diseases like multiple sclerosis. Using an end-user guided approach, it will facilitate responsible and critical assessment of the use of AI in healthcare. 2023-2028 Chronic immune-mediated diseases Horizon Europe DATA MANAGEMENT INFRASTRUCTURE EUCAIM | EUropean Federation for CAncer IMages is a project that will build a highly secure, federated and large-scale European cancer imaging platform, with capabilities that will greatly enhance the potential of Artificial Intelligence in oncology. 2023-2027 Cancer Digital Europe Programme (DIGITAL) DISCOVERY CONTAGIO | CONTAGIO (COhorts Network To be Activated Globally In Outbreaks) aims to create coordination mechanisms to rapidly react to infectious disease (re-)emergence in low- and middle-income countries (LMICs). 2023-2026 Infectious Diseases European Commission - Horizon Europe ACCESS DATA MANAGEMENT DISCOVERY Youth-GEMs | Youth-GEMS (Gene Environment Interactions in Mental Health TrajectorieS of Youth) will conduct research into the genetic and environmental factors of mental health in young European people. 2022-2027 Mental health European Commission - Horizon Europe DATA MANAGEMENT DISCOVERY GDI | The European Genomics Data Infrastructure project is enabling access to genomic and related phenotypic and clinical data across Europe. It is doing this by establishing a federated, sustainable and secure infrastructure to access the data. 2022-2026 Genomic and health data European Commission - Horizon Europe; "La Caixa" Foundation cofunds CRG's contribution DISCOVERY DOCUMENTATION INFRASTRUCTURE EOSC4Cancer | EOSC4Cancer builds on existing projects, research outcomes and established community solutions to create the federated FAIR data, analysis and services infrastructure needed for European Cancer research programmes. 2022-2025 Cancer European Commission - Horizon Europe DISCOVERY IMPaCT-T2D | The IMPaCT-T2D project aims at studying the complete genomes of a large cohort of patients with Type 2 Diabetes mellitus (T2D), using modern sequencing technologies and artificial intelligence (AI) in order to improve the stratification and pharmacological treatment in the context of precision medicine. 2022-2025 Cardiovascular and Complex Diseases Spanish Ministry of Science and Innovation; Instituto de Salud Carlos III ACCESS DATA MANAGEMENT DISCOVERY INFRASTRUCTURE EuCanImage | A European Cancer Image Platform Linked to Biological and Health Data for Next-Generation Artificial Intelligence and Precision Medicine in Oncology. 2020-2025 AI Solutions in Oncology European Commission - H2020 Programme; "La Caixa" Foundation cofunds CRG's contribution DATA MANAGEMENT METADATA STANDARDS GenoMed4ALL | A consortium built to empower personalised medicine in the field of haematological diseases through the use of AI and the pooling of genomic and clinical data. 2020-2025 Hematological diseases European Commission - H2020 Programme DISCOVERY METADATA STANDARDS Completed projects Project Duration Domain Funder Tags BY-COVID | The BeYond-COVID project aims to make COVID-19 data accessible to scientists in laboratories but also to anyone who can use it, such as medical staff in hospitals or government officials. Going beyond SARS-CoV-2 data, the project will provide a framework for making data from other infectious diseases open and accessible to everyone. 2021-2024 Infectious diseases European Commission - H2020 Programme ACCESS DATA MANAGEMENT DISCOVERY INFRASTRUCTURE IMPaCT-Data | IMPaCT-Data aims to create the infrastructure for secondary use of data from Spanish healthcare systems - electronic health records, medical imaging and genomic repositories - and contribute with the knowledge and methodology produced to the healthcare system. 2021-2024 Large-scale genomics and health dataSpanish Ministry of Science and Innovation; Instituto de Salud Carlos III ACCESS DATA MANAGEMENT DISCOVERY INFRASTRUCTURE LaMarató | It is a project aimed at creating and developing a catalan interhospitalary network to interrogate genetic variants from thousands of genetic tests carried out in patients with rare diseases from the main catalan hospitals. 2021-2024 Genomic and health data Fundació La Marató de TV3 (catalan foundation) DISCOVERY HealthyCloud | This consortium will contribute a Strategic Agenda towards the European Health Research and Innovation Cloud. The project will work in collaboration with a broad range of stakeholders to ensure that all voices are included and that the results are technically and ethically sound. 2021-2023 Not Applicable European Commission - H2020 Programme DOCUMENTATION B1MG | Beyond 1 Million Genomes aims to create a network of genetic and clinical data across Europe. The project provides coordination and support to the 1+ Million Genomes Initiative (1+MG). This initiative is a commitment of 24 EU countries, the UK and Norway to give cross-border access to one million sequenced genomes by 2022. 2020-2023 Not applicable European Commission - Horizon Europe DATA MANAGEMENT INFRASTRUCTURE METADATA STANDARDS ELIXIR-CONVERGE | An alliance with the goal of Connecting and aligning ELIXIR Nodes to deliver sustainable FAIR life-science data management services. 2020-2023 Data Management and Infectious Diseases European Commission - H2020 Programme DATA MANAGEMENT INFRASTRUCTURE METADATA STANDARDS IHCC | The International HundredK+ Cohorts Consortium aims to create a global platform for translational research – informing the biological and genetic basis for disease and improving clinical care and population health. 2020-2022 Translational research NIH; The Wellcome Trust; CZI INFRASTRUCTURE METADATA STANDARDS PPCG | The Pan Prostate Cancer Group aims to harmonise and interrogate Whole Genome DNA Sequence data generated around the world from over 2000 men with prostate cancer, with associated transcriptome and methylome data to include men from different clinical categories, and ethnicities. This project is about providing breakthrough advances through analysis of a very large series of Whole Genome DNA data from prostate cancer contributed by many of the leading scientists and clinicians working in prostate cancer genomics. 2019-2024 Cancer Cancer Research UK DATA MANAGEMENT CINECA | Consortium providing a Federated solution enabling population-scale genomic and biomolecular data accessible across international borders accelerating research and improving the health of individuals resident across continents. 2019-2023 Large-scale Genomics and Health Data European Commission - H2020 Programme ACCESS DATA MANAGEMENT DISCOVERY INFRASTRUCTURE EASI-Genomics | A project designed to provide easy access to cutting-edge DNA sequencing technologies to researchers from academia and industry, within a framework that ensures compliance with ethical and legal requirements, as well as FAIR and secure data management. 2019-2023 Next Generation Sequencing European Commission - H2020 Programme ACCESS EJP-RD | An European consortium built to create a comprehensive, sustainable ecosystem allowing a virtuous circle between research, care, and medical innovation. 2019-2023 Rare diseases European Commission - H2020 Programme ACCESS DATA MANAGEMENT DOCUMENTATION METADATA STANDARDS EOSC-Life | EOSC-Life brings together the 13 Life Science research infrastructures (LS RIs) to create an open, digital and collaborative space for biological and medical research. The project will publish 'FAIR' data and a catalogue of services provided by participating RIs for the management, storage and reuse of data in the European Open Science Cloud (EOSC). 2019-2023 Not applicable European Commission - H2020 Programme DOCUMENTATION EUCANCan | A federated network aiming at implementing a cultural, technological and legal integrated framework across Europe and Canada, to enable and facilitate the efficient sharing of cancer genomic data. 2019-2023 Cancer European Commission - H2020 Programme DATA MANAGEMENT METADATA STANDARDS The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes | This project is a direct continuation of the FHD IS with the goal to position the FEGA framework as the core infrastructure driver to support human data sharing for research. 2019-2023 Human genomic data ELIXIR INFRASTRUCTURE UK Biobank | UK Biobank is a large-scale biomedical database and research resource, containing in-depth genetic and health information from half a million UK participants. This project is to archive whole genome sequencing and other genetic data for UK Biobank participants. 2019-2023 Large-scale Genomics and Health Data The Wellcome Trust; UKRI; Amgen; AstraZeneca; GSK; Johnson & Johnson DATA MANAGEMENT INFRASTRUCTURE VEIS | The core mission of VEIS is to create an open ecosystem of technologies that will address and adapt to the requirements of the systems used to analyse and interpret -omics and clinical data in research and application environments in biomedicine. The aim of the project is to leverage the value of the EGA for both industry and society. 2019-2022 Oncology and Rare diseases Generalitat de Catalunya and European Regional Development Fund (ERDF) ACCESS DISCOVERY ELIXIR BEACON IS | This study follows on from a number of earlier activities that have established the ELIXIR Beacon Project. The main aim is to extend the Beacon protocol, developed at EGA, to become the reference ELIXIR Data Discovery product 2019-2021 Not applicable ELIXIR DISCOVERY ELIXIR FHD IS | This project coordinates the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. 2019-2021 Human genomic data ELIXIR INFRASTRUCTURE ELIXIR Rare Disease | The Rare Disease Community extends and generalises the system of access authorisation and high volume secure data transfer developed within the EGA. The goal of the Community is to create a federated infrastructure that will enable researchers to discover, access and analyse different rare disease repositories across Europe. It is doing this in partnership with other European infrastructure projects, namely RD-CONNECT, BBMRI-ERIC and E-Rare.2019-2021 Rare diseases ELIXIR INFRASTRUCTURE Solve-RD | Solve-RD - solving the unsolved rare diseases - is a research project funded by the European Commission. It echoes the ambitious goals set out by the International Rare Diseases Research Consortium (IRDiRC) to deliver diagnostic tests for most rare diseases by 2020. The current diagnostic and subsequent therapeutic management of rare diseases is still highly unsatisfactory for a large proportion of rare disease patients - the unsolved RD cases. For these unsolved rare diseases, we are unable to explain the etiology responsible for the disease phenotype, predict the individual disease risk and/or rate of disease progression, and/or quantitate the risk of relatives to develop the same disorder. 2018-2024 Rare diseases European Commission - H2020 Programme ACCESS DATA MANAGEMENT METADATA STANDARDS EuCanShare | An EU-Canada joint infrastructure for next-generation multi-Study Heart research. 2018-2022 Cardiovascular Diseases European Commission - H2020 Programme ACCESS METADATA STANDARDS

Documentation about/projects-and-funders/projects

LuCaP cell line ChIP-seq

ChIP-seq of 2 LuCaP cell lines with different factors. LuCaP cell line 189.4 was ChIP-sequenced for 6 factors with different conditions as well as the input DNA (n=31 in total). LuCaP 189.4 ChIP-sequence experiments include; 3 H3K27ac/DMSO, 3 H3K27ac/vorinostat, 3 H3K27ac/dexamethasone, 3 H3K27ac/dexamethasone/vorinostat, 3 GR dexamethasone, 3 GR dexamethasone/vorinostat, 3 HDAC3/DMSO, 3 AR, 3 FOXA1, 3 H3K27ac and 1 input sample. LuCaP 35 ChIP-sequence experiments as well as input include (n=10 in total); 3 H3K27ac, 3 AR, 3 FOXA1 and 1 input sample. All 41 samples were sequenced using paired-end reads on Illumina NovaSeq 6000. Each sample has 2 fastq files, one for the forward and reverse read, respectively.

Dataset EGAD50000001345

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

Single-cell RNA sequencing of chemotherapy-resistant muscle-invasive urothelial bladder cancer

All single-cell mRNA sequencing data were acquired from a single patient (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib).

Study EGAS00001004233

Germline HAVCR2 mutations altering TIM-3 characterize subcutaneous panniculitis-like T-cell lymphomas with hemophagocytic lymphohistiocytic syndrome

Sub-cutaneous panniculitis-like T-cell lymphomas (SPTCL), a non-Hodgkin lymphoma, can be associated with hemophagocytic lymphohistiocytosis (HLH), a life-threatening immune activation which adversely impacts survival1,2. T-cell-immunoglobulin mucin-3 (TIM-3) is a modulator of immune responses expressed on subgroups of T- and innate immune cells. We identify in ~60% of SPTCL cases germline, loss-of-function, missense variants in highly conserved residues of TIM-3, c.245A>G(p.Y82C) and c.291A>G(p.I97M), each with specific geographic distribution. Y82C-TIM-3 occurs on a potential founder chromosome in patients with East Asian and Polynesian ancestry, while I97M-TIM-3 occurs in Caucasians. Both variants induce protein misfolding and abrogate TIM-3’s plasma-membrane expression leading to persistent immune activation, increased production of inflammatory cytokines, including TNF-α and IL-1β, promoting HLH and SPTCL. Our findings highlight HLH/SPTCL as a new genetic entity and showcase TIM-3 mutations as the first causative genetic defect in SPTCL. While TIM-3-mutant HLH/SPTCL benefit from immunomodulation, therapeutic repression of the TIM-3 checkpoint may have adverse consequences.

Study EGAS00001002765

Ribo-depleted RNA-sequencing of II.3, III.1, and III.3

This datasets contains the Ribo-depleted RNA-sequencing of patients II.3, III.1, and III.3. Libraries were sequenced to a minimum depth of 195 million read pairs (2x75nts) on an Illumina NextSeq500 Midoutput FC.

Dataset EGAD50000002364

BLUEPRINT September 2016, ATAC-seq for naive B cell from tonsil, on Genome GRCh38

ATAC-seq data for 3 sample(s) for naive B cell from tonsil, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

Dataset EGAD00001002903

BLUEPRINT September 2016, ATAC-seq for unswitched memory B cell from venous blood, on Genome GRCh38

ATAC-seq data for 3 sample(s) for unswitched memory B cell from venous blood, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

Dataset EGAD00001002905

BLUEPRINT September 2016, ATAC-seq for naive B cell from venous blood, on Genome GRCh38

ATAC-seq data for 3 sample(s) for naive B cell from venous blood, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

Dataset EGAD00001002902

Spinocerebellar ataxia type 3 RNA-sequencing study

RNA-Sequencing from human post-mortem Spinocerebellar ataxia type 3 patients. This sequencing experiment was carried out to validate that the transcriptional changes of an Ataxin-3 knock-in mouse model (expressing an expansion of 304 CAG/CAAs either heterozygous or homozygous in the murine Ataxin-3 locus) represent that transcriptional changes seen in the human disease.

Study EGAS00001004241

BLUEPRINT release August 2016, DNase-Hypersensitivity for inflammatory macrophage, on genome GRCh38

DNase-Hypersensitivity data for 3 inflammatory macrophage sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816

Dataset EGAD00001002374

BLUEPRINT release August 2015, DNase-Hypersensitivity for inflammatory macrophage, on genome GRCh38

DNase-Hypersensitivity data for 3 inflammatory macrophage sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820

Dataset EGAD00001001573

BLUEPRINT release August 2016, DNase-Hypersensitivity for erythroblast, on genome GRCh38

DNase-Hypersensitivity data for 3 erythroblast sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816

Dataset EGAD00001002350

scRNAseq of ARID1B+/+ (control) and ARID1B+/- human telencephalic organoids at D120

This dataset contains scRNAseq data of human telencephalic organoids, at day 120, from 4 different sequencing runs (libraries), as follows (please see cell line clone nomenclature in original publication): 1. Library 177136: Pat.2 ARID1B+/+ clone 2c (2 organoids, E11rep_1, E11rep_2), Pat.2 ARID1B+/- clone 2a (2 organoids: B002orig_1, B002orig_2) 2. Library 178119: Pat.2 ARID1B+/+ clone 2c (3 organoids: E11rep_1, E11rep_2, E11rep_3), Pat.2 ARID1B+/- clone 2a (3 organoids: B002orig_1, B002orig_2, B002orig_3) 3. Library 178120: Pat.2 ARID1B+/+ clone 2d (3 organoids: A3rep_1, A3rep_2, A3rep_3), Pat.2 ARID1B+/- clone 2b (3 organoids: B002_F7_1, B002_F7_2, B002_F7_3) 4. Library 184337: Pat.1 ARID1B+/- clone 1a (3 organoids: B001orig_1, B001orig_2, B001orig_3), HD.1 ARID1B+/+ clone 3a (3 organoids: 176_1, 176_2, 176_3), HD.1 ARID1B+/- clone 3b (3 organoids: F10_1, F10_2, F10_3)

Dataset EGAD50000000498

High coverage Whole exome DNA sequencing on pre-treatment tumor samples (n=3) matched with post-treatment metastasized lymph nodes isolated with laser microdissection (n=3)

Data from NABUCCO cohort 1 (NCT03387761). This dataset includes High coverage Whole exome DNA sequencing on pre-treatment bladder tumor samples (n=3) matched with post-treatment metastasised adjacent lymph nodes isolated with laser microdissection (n=3) for 3 unique patients

Dataset EGAD00001006852

BLUEPRINT release August 2014, RNA-Seq for common myeloid progenitor

RNA-Seq data for 3 common myeloid progenitor sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

Dataset EGAD00001000907

BLUEPRINT release January 2015, RNA-Seq for common myeloid progenitor

RNA-Seq data for 3 common myeloid progenitor sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

Dataset EGAD00001001169

Whole exome sequencing of peripheral T-cell lymphoma (PTCL)

Somatic mutations in 3 AITL and 3 PTCL, not otherwise specified (PTCL-NOS) specimens were explored using whole-exome sequencing.

Study EGAS00001000557

2197 results for "盛和资源+机构评级+2026年3月最新"

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