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Single-cell G&T sequencing - Genomic data

Single-cell G&T seq from an untreated PDX mouse with neuroblastoma (MYCN amplified).

Request Access

DUO:0000018
version: 2021-02-23

not for profit, non commercial use only

This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.

DUO:0000021
version: 2021-02-23

ethics approval required

This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval.

DUO:0000026
version: 2021-02-23

user specific restriction

This data use modifier indicates that use is limited to use by approved users.

Data access agreement to access Berlin neuroblastoma single-cell cohort

DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom the Berlin Neuroblastoma single-cell DAC (Prof. Dr. Henssen) grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: Prof. Dr. Henssen and the collaborators listed in Appendix I responsible for the development, organization, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. DAC: Berlin Neuroblastoma single-cell DAC Prof. Dr. Henssen: Department of Pediatric Oncology, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. The User Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognizing the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution agrees to follow the following Publication Policy: In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with the Berlin Neuroblastoma single-cell DAC. 9. The User Institution agrees not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (http://www.oecd.org/science/biotech/36198812.pdf ). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify the DAC within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify the DAC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The DAC may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than Prof. Dr. Henssen. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorized Personnel. The User Institution will procure that the Authorized Personnel comply with the terms of this agreement. 19. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of the Federal Republic of Germany. Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for the Berlin Neuroblastoma single-cell DAC Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) Name of project that created the dataset Names of other data producers/collaborators Specific limitations on areas of research Minimum protection measures required File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screen locks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (500 words max) All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* All Individuals that should have an account created at the EGA Name of Registered User Email Job Title

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000001040 Cancer Genomics

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
EGAF50000380728 bam 299.0 MB
EGAF50000380729 bam 3.8 MB
EGAF50000380730 bam 1.6 MB
EGAF50000380731 bam 316.7 MB
EGAF50000380732 bam 343.1 MB
EGAF50000380733 bam 336.4 MB
EGAF50000380734 bam 377.1 MB
EGAF50000380735 bam 256.9 MB
EGAF50000380736 bam 319.5 MB
EGAF50000380737 bam 272.5 MB
EGAF50000380738 bam 236.8 MB
EGAF50000380739 bam 236.0 MB
EGAF50000380740 bam 257.9 MB
EGAF50000380741 bam 339.5 MB
EGAF50000380742 bam 243.2 MB
EGAF50000380743 bam 106.1 MB
EGAF50000380744 bam 358.8 MB
EGAF50000380745 bam 541.3 MB
EGAF50000380746 bam 373.9 MB
EGAF50000380747 bam 121.9 kB
EGAF50000380748 bam 251.1 MB
EGAF50000380749 bam 410.0 MB
EGAF50000380750 bam 182.3 MB
EGAF50000380751 bam 321.9 MB
EGAF50000380752 bam 344.8 MB
EGAF50000380753 bam 258.0 MB
EGAF50000380754 bam 311.0 MB
EGAF50000380755 bam 5.2 MB
EGAF50000380756 bam 362.0 MB
EGAF50000380757 bam 281.2 MB
EGAF50000380758 bam 317.1 MB
EGAF50000380759 bam 10.7 MB
EGAF50000380760 bam 549.9 MB
EGAF50000380761 bam 221.3 MB
EGAF50000380762 bam 208.1 MB
EGAF50000380763 bam 4.7 MB
EGAF50000380764 bam 295.8 MB
EGAF50000380765 bam 504.7 MB
EGAF50000380766 bam 261.9 MB
EGAF50000380767 bam 195.5 MB
EGAF50000380768 bam 246.8 MB
EGAF50000380769 bam 212.6 MB
EGAF50000380770 bam 485.6 MB
EGAF50000380771 bam 5.9 MB
EGAF50000380772 bam 3.1 MB
EGAF50000380773 bam 145.5 MB
EGAF50000380774 bam 256.9 MB
EGAF50000380775 bam 388.6 MB
EGAF50000380776 bam 8.0 MB
EGAF50000380777 bam 355.9 MB
EGAF50000380778 bam 5.8 MB
EGAF50000380779 bam 209.9 MB
EGAF50000380780 bam 992.9 kB
EGAF50000380781 bam 331.6 MB
EGAF50000380782 bam 363.1 MB
EGAF50000380783 bam 282.8 MB
EGAF50000380784 bam 197.7 MB
EGAF50000380785 bam 269.1 MB
EGAF50000380786 bam 274.4 MB
EGAF50000380787 bam 285.6 MB
EGAF50000380788 bam 459.0 MB
EGAF50000380789 bam 377.2 MB
EGAF50000380790 bam 357.4 MB
EGAF50000380791 bam 160.6 MB
EGAF50000380792 bam 264.0 MB
EGAF50000380793 bam 9.9 MB
EGAF50000380794 bam 411.0 MB
EGAF50000380795 bam 38.4 kB
EGAF50000380796 bam 251.6 MB
EGAF50000380797 bam 159.2 MB
EGAF50000380798 bam 354.9 MB
EGAF50000380799 bam 307.0 MB
EGAF50000380800 bam 351.1 MB
EGAF50000380801 bam 10.2 MB
EGAF50000380802 bam 2.0 GB
EGAF50000380803 bam 151.0 MB
EGAF50000380804 bam 315.6 MB
EGAF50000380805 bam 313.5 MB
EGAF50000380806 bam 397.3 MB
EGAF50000380807 bam 8.4 MB
EGAF50000380808 bam 173.6 MB
EGAF50000380809 bam 284.9 MB
EGAF50000380810 bam 376.6 MB
EGAF50000380811 bam 5.2 MB
EGAF50000380812 bam 288.0 MB
EGAF50000380813 bam 485.2 MB
EGAF50000380814 bam 133.3 MB
EGAF50000380815 bam 27.6 MB
EGAF50000380816 bam 1.1 MB
EGAF50000380817 bam 242.4 MB
EGAF50000380818 bam 311.9 MB
EGAF50000380819 bam 3.2 MB
EGAF50000380820 bam 3.4 MB
EGAF50000380821 bam 183.0 MB
EGAF50000380822 bam 3.9 MB
EGAF50000380823 bam 286.5 MB
96 Files (24.3 GB)