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• Privacy Notice for EGA Web user

  Privacy Notice for EGA Public Website This Privacy Notice explains what personal data is collected by the specific service you are requesting, for what purposes, how it is processed, and how we keep it secure. 1. Who controls your personal data and how to contact us? European Genome- Phenome Archive - EGA offers a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects, jointly managed by European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI) and Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG). EMBL-EBI and CRG represent joint Data Controllers’ of processing of your personal data. They and their Data protection officers may be contacted for data protection queries and for exercising your rights under Section 8. You may contact EMBL-EBI, represented by Mallory Freeberg, by: email at: mfreeberg@ebi.ac.uk , or post at EMBL-EBI, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridgeshire, UK. EMBL’s Data Protection Officer may be contacted by: telephone at +49 6221 387-8590, email at dpo@embl.org , or post at EMBL Heidelberg, Data protection officer, Meyerhofstraße 1, 69117 Heidelberg, Germany. You may contact CRG, whose EGA team is represented by dr. Jordi Rambla de Argila, by: email at jordi.rambla@crg.eu, or post at Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG), Dr.Aiguader 88, PRBB Building, 08003 Barcelona, Spain. CRG Data protection officer may be contacted by: email at dpo@crg.eu post at Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, PRBB Building, 08003 Barcelona, Spain. 2. Which is the lawful basis for processing personal data? For providing you access to the website and for offering support whilst using the website, we need your consent under Article 5 (2) of the IP 68 (equivalent to Article 6 (1)(a) of the GDPR). For monitoring your activities on the website, we process your personal data on the grounds of important public interest. Such legal basis is found in Article 5(1)(a) of EMBL Internal Policy No 68 on General Data Protection (hereinafter IP 68), which is equivalent to Article 6 (1)(e) of the EU General Data Protection Regulation (hereinafter GDPR) and upon which personal data are processed for the achievement of the aims laid down in 1973 agreement establishing EMBL, such as the promotion of the cooperation in the fundamental research, in the development of advanced instrumentation and in advanced teaching in molecular biology and dissemination of information. 3. What personal data is collected from users of the service? How do we use this personal data? We collect the following personal data from you: IP addressesDate and time of a visit to the service website Operating systemAmount of data transmittedBrowserEmail address (only when support is requested by the user) The data controller will use your personal data for the following purposes: To provide the user access to the serviceTo better understand the needs of the users and guide future improvements of the serviceTo monitor website activities according to and in compliance with the Terms of UseTo better understand the needs of the website visitors and guide future improvements of the serviceTo conduct and monitor website security activitiesTo create anonymous usage statistics 4. Who will have access to your personal data? The personal data will be disclosed to: Authorised staff in the data controller’s institutions acting on data controller`s behalf and instructions. 5. Will your personal data be transferred to third countries (i.e. countries not part of EU/EEA) and/or international organisations? There are no personal data transfers to third countries or international organisations. 6. How long do we keep your personal data? Any personal data directly obtained from you will be retained as long as the service is live. Such duration serves the purpose of enabling scientific research and ensures legal compliance and facilitates internal and external audits if they arise. By contrast, the log files for the data categories related to anonymous usage statistics (raw web service logs) are processed only for 30 days and thereafter erased. 7. The joint Data Controllers provide these rights regarding your personal data You have the right to: Not be subject to decisions based solely on an automated processing of data (i.e. without human intervention) without you having your views taken into consideration.Request at reasonable intervals and without excessive delay or expense, information about the personal data processed about you. Under your request we will inform you in writing about, for example, the origin of the personal data or the preservation period.Request information to understand data processing activities when the results of these activities are applied to you.Object at any time to the processing of your personal data unless we can demonstrate that we have legitimate reasons to process your personal data.Request free of charge and without excessive delay rectification or erasure of your personal data if we have not been processing it respecting the data protection policies of the respective controllers. It must be clarified that rights under points 4 and 5 are only available whenever you need support whilst using our website. For other processing based on the grounds of important public interest you cannot exercise your rights to object, rectify or erase your personal data according to the Article 13(2)(a)(b) of IP 68 (equivalent to Article 17(3)(b)(d) and Article 21(6) of the GDPR). 8. Supervisory authority If you wish to complain against the processing of your personal data, you may do so by post at: EMBL Heidelberg, Data Protection Committee, Meyerhofstraße 1, 69117 Heidelberg, Germany, or Autoritat Catalana de Protecció de Dades (Catalan Data Protection Authority), C/Rosselló 214, Esc A, 1r 1a, Barcelona 08008, Spain. 9. CookiesWe use cookies and similar technologies that are strictly necessary for the correct functioning and security of the EGA website (for example, to enable core site features and to help protect the service). These cookies do not store information that directly identifies you.You can set your browser to block or delete cookies. Please note that if you disable strictly necessary cookies, parts of the website may not function properly.Published on February 6, 2019

  Documentation data-protection/privacy-notice/ega-website

• Tissue Site

  Tissue site for RNAsequencing data. Tissue site is associated with the clinical biomarker data and be linked to the biomarker data using the SAMPLE and PAT identifiers.

  Dataset EGAD50000000931

• Whole-genome sequencing

  Variant calls from whole-genome sequencing of Ly1-07 using Complete Genomics paired-end sequencing service.

  Dataset EGAD00001004783

• Link to the Finnish FEGA Node's service provider

  We would like to direct you to the service provider for the Finnish FEGA Node, which is CSC – IT Center for Science (https://research.csc.fi/-/fega). It's important to note that this is not a genuine DAC and does not serve as the data controller. To obtain access to data stored in FI-FEGA, it is essential to utilize the local access management system SD Apply. Please be aware that applications submitted through the EGA DAC portal will not be processed. For a seamless experience, we kindly request you to refer to the policy of your selected dataset and submit your access application through SD Apply (https://sd-apply.csc.fi/). Your cooperation is highly appreciated.

  Dac EGAC50000000022

• T cell transcriptional gradient

  There are two datasets: 1. scRNA-seq of human cutaneous immune cells from psoriasis patients. These include pre- and post-Tildrakizumab treated patients and come in a BAM file format. 19006FL-25-01 19006FL-38-01 19006FL-32-01-03 19006FL-33-01 19006FL-28-01-05 19006FL-35-01-01 2. RNA-seq of ZFP36L2 CRISPIR deleted Human T cells are FASTQ files. 19006XR-30-05 19006XR-30-04 19006XR-30-02 19006XR-30-01 19006XR-26-05 19006XR-26-04 19006XR-26-02 19006XR-26-01 19006R-22-04 19006R-22-08 19006R-22-05 19006R-22-01

  Dataset EGAD00001009677

• DAC-2020-03-26-Lemola (DAC-039))

  DAC-2020-03-26-Lemola (DAC-039)), raw data in EGA, metadata in Harvard Dataverse

  Dataset EGAD50000000897

• Genome-wide evaluation of the maturation of the immune response to the tuberculin skin test from day 2 to day 7

  The tuberculin skin test (TST) is a standardised human challenge model to evaluate the immune response to Mycobacterium tuberculosis (Mtb) antigens in vivo. To study the temporal evolution of the TST, we recruited healthy volunteers with evidence of peripheral blood Mtb reactive T cells, to undergo a TST in each arm that was sampled on day 2 at one site and on day 7 at the contralateral site on day 7. Genome-wide TST transcriptomes at day 2 and day 7 were defined by differential gene expression compared to transcriptomes from the site of control saline injections performed in a separate subset of volunteers.

  Study EGAS50000000822

• National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS)

  NIAGADS is an NIH controlled-access data repository that collaborates with researchers around the world to facilitate data access and sharing for genomic and associated omics data related to Alzheimer's Disease (AD), Alzheimer's Disease Related Dementias (ADRD), as well as healthy aging. Serving as the data coordinating center for the Alzheimer's Disease Sequencing Project (ADSP), NIAGADS hosts all ADSP-generated whole-exome, whole-genome and associated phenotypes. Other data types hosted by NIAGADS include genotype SNP arrays, functional omics, fluid biomarkers, aggregated imaging data (such as volumetric data for brain regions of interest), and summary statistics. In adherence with NIH security best practices and genome data sharing policies, NIAGADS supports data access requests through review by an NIH-appointed and registered Data Access Committee. Data stored within NIAGADS cannot be requested via dbGaP. Data requests must go through the NIAGADS Data Sharing Service (DSS) via the following NIAGADS url: https://dss.niagads.org/. Questions related to the request of data should be directed to the NIAGADS admin team at: niagads@pennmedicine.upenn.edu. DSS is a FISMA certified platform built by a team of data scientists at the University of Pennsylvania to support the request and access of AD/ADRD data by qualified researchers internationally. Questions related to the use of data hosted in the DSS should be directed to the Portal admin team at: help@niagads.org.

  Study phs004180

• Targeted sequencing of Burkitt lymphoma tumour samples from the UK's Haematological Malignancy Research Network

  The UK’s Haematological Malignancy Research Network (www.HMRN.org) was established in 2004 to provide robust generalizable data to inform clinical practice and research. HMRN is a collaboration between researchers in the Epidemiology & Statistics Group (ECSG) at the University of York, a unified Clinical Network operating across 14 hospitals, and an integrated Haematological Malignancy Diagnostic Service (HMDS) in Leeds. Covering a population of around 4 million, HMRN collects detailed information about all patients diagnosed with a haematological malignancy within the HMRN region, accruing around 2,400 new diagnoses each year. The population has a similar socio-demographic profile to the country as a whole, and HMRN’s maturing data present an increasingly valuable resource to address real questions of concern to haematologists, commissioners and health service researchers – locally, nationally and internationally. This study forms part of a larger project employing targeted exome sequencing on tumour samples from patients diagnosed with a variety of both lymphoid and myeloid malignancies. The results for samples collected from 39 Burkitt lymphoma patients, diagnosed within HMRN from 2005 to 2012, are provided.

  Study EGAS00001004649

• WGS of Multiple Myeloma/MGUS/SMM cases (germline) - VCF files (SNPs)

  WGS - PCR-free library preparation (whole blood gDNA), paired-end (2x100bp) sequencing on DNBseq sequencing platform (BGI) Number of samples: 26

  Dataset EGAD50000001800