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Whole genome sequencing of acute erythroid erythroid leukemia

Briefly, twenty paired tumor and germline DNAs were extracted from patients’ BM and from buccal mucosa, respectively. Samples were subjected to massively parallel sequencing using the HiSeq 2000, HiSeq2500, HiSeq X Ten, and/or NovaSeq 6000 according to the manufacturer’s instructions. Sequencing reads were aligned to NCBI Human Reference Genome Build 37 (hg19) by Burrows−Wheeler Aligner, version 0.7.10, with default parameters (http://bio-bwa.sourceforge.net/). PCR duplicates were eliminated using Picard tools version 1.39 (GATK).

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Data policy of sequencing data of acute erythroid leukemia

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 Department of Pathology and Tumor Biology, Kyoto University Data Access Committee 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: Department of Pathology and Tumor Biology, Kyoto University 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. 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 recognising 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 Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 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 Department of Pathology and Tumor Biology, Kyoto University Data Access Committee within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Department of Pathology and Tumor Biology, Kyoto University Data Access Committee prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Department of Pathology and Tumor Biology, Kyoto University Data Access Committee as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Department of Pathology and Tumor Biology, Kyoto University Data Access Committee 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 Department of Pathology and Tumor Biology, Kyoto University. 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 Authorised Personnel. The User Institution will procure that the Authorised 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 Japan and shall be subject to the exclusive jurisdiction of the Japanese courts.

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
Other

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 Located in
EGAF00005719895 1637398500274 48.9 GB
EGAF00005719896 1637397720133 67.4 GB
EGAF00005719897 1637409937832 121.3 GB
EGAF00005719898 1637406300063 92.7 GB
EGAF00005719899 1637400841517 87.8 GB
EGAF00005719900 1637405161231 63.7 GB
EGAF00005719901 1637408341092 88.2 GB
EGAF00005719902 1637406481108 68.3 GB
EGAF00005719903 1637407920028 86.3 GB
EGAF00005719904 1637405401419 86.7 GB
EGAF00005719905 1637398141565 47.9 GB
EGAF00005719906 1637402350654 76.9 GB
EGAF00005719907 1637404980042 47.3 GB
EGAF00005719908 1637399318319 57.2 GB
EGAF00005719909 1637408101087 73.3 GB
EGAF00005719910 1637401800442 77.6 GB
EGAF00005719911 1637399640404 58.1 GB
EGAF00005719912 1637398440522 66.8 GB
EGAF00005719913 1637401560890 125.9 GB
EGAF00005719914 1637408700029 85.9 GB
EGAF00005719915 1637402845885 78.8 GB
EGAF00005719916 1637403300185 74.8 GB
EGAF00005719917 1637407080025 57.4 GB
EGAF00005719918 1637399318319 59.4 GB
EGAF00005719919 1637408700029 86.1 GB
EGAF00005719920 1637399700369 75.4 GB
EGAF00005719921 1637402845885 51.6 GB
EGAF00005719922 1637399640404 53.4 GB
EGAF00005719923 1637402220457 49.8 GB
EGAF00005719924 1637400720388 72.1 GB
EGAF00005719925 1637400121451 59.4 GB
EGAF00005719926 1637400900524 64.9 GB
EGAF00005719927 1637406300063 58.3 GB
EGAF00005719928 1637404141407 88.9 GB
EGAF00005719929 1637405281580 122.6 GB
EGAF00005719930 1637407201235 79.6 GB
EGAF00005719931 1637405281580 58.2 GB
EGAF00005719932 1637401328347 85.9 GB
EGAF00005719933 1637405700117 64.2 GB
EGAF00005719934 1637403961414 55.4 GB
40 Files (2.9 TB)