Oxford Nanopore targeted RNA-based amplicon data of 12 classical HLA genes

The dataset consists of Oxford Nanopore targeted RNA-based amplicon data of 12 classical HLA genes (HLA-A, -B, -C, -DRA, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, and DPB1) of 50 healthy individuals. The 12 classical genes were sequenced in two separate gene pools on R9.4 flowcells using MinION sequencer. Per individual, gene pool 1 contains HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, and -DPB1 and gene pool 2 HLA-DRA, -DQA1, -DQB1, and -DPA1. The dataset includes 100 fastq files of Oxford Nanopore 2D reads (50 for gene pool 1 and 50 for gene pool 2).

100 samples
DAC: EGAC00001001877
Technology: MinION

Access Policy1 Study Files

Metadata

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The Data Access Agreement policy for the Oxford Nanopore RNA sequencing data owned by the Finnish Red Cross Blood Service (FRCBS).

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. 1. Definitions Authorized Personnel: The individuals at the User Institution to whom FRCBS 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 Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data may include personal data as defined in the EU General Data Protection Regulation (2016/679) (“GDPR”). Data Producers: FRCBS 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: non-commercial 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 at the User Institution 2. Terms and Conditions 2.1. 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. 2.2. The User Institution agrees to use all reasonable efforts 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. 2.3. The User Institution agrees to use reasonable efforts to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking reasonable care to limit the possibility of identification. 2.4. 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. 2.5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorized 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. 2.6. 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. Notwithstanding the above, the User Institution will not be responsible for claims arising from or related to the negligence or willful misconduct of the Data Producers, other parties involved in the creation, funding or protection of these Data, or their officers, agents or employees, or any person or entity not subject to User Institution’s supervision or control. 2.7. The User Institution agrees to follow the Fort Lauderdale Guidelines (attached as Appendix IV) and the Toronto Statement (as attached in Appendix III). 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. 2.8. 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 analyzing these Data. 2.9. 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. 2.10. 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 non-commercial research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (attached as Appendix V ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (attached as Appendix VI). 2.11. 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. 2.12. The User Institution will notify FRCBS within 30 days of any changes or departures of Authorized Personnel. 2.13. The User Institution will notify FRCBS prior to any significant changes to the protocol for the Project. 2.14. The User Institution will promptly notify FRCBS should it become aware of a breach of the terms or conditions of this agreement. 2.15. Either Party may terminate this agreement for any reason by provided thirty (30) days prior written notice to the other Party. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. 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. Any such changes shall be implemented upon execution of a dually signed amendment to this Agreement. 2.16. If requested, upon advance written notice, and to the extent necessary, during mutually agreeable normal administrative business hours 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. Any such visits shall be scheduled in coordination with User Institution, and shall be subject to compliance with User Institution’s reasonable measures for confidentiality, safety and security, and shall also be subject to compliance with generally applicable premises rules at User Institution. 2.17. The User Institution agrees to distribute a copy of these terms to the Authorized Personnel. The User Institution will require that the Authorized Personnel comply with the terms of this agreement. 2.18. The User Institution understands that upon receipt of the Data that includes or constitutes Personal Data, it will become a data controller as meant in the General Data Protection Regulation (2016/679) (“GDPR”). 2.19. IF THE USER INSTITUTION IS NOT LOCATED WITHIN THE EEA / A COUNTRY WITH AN ADEQUACY DECISION: As a data controller, the User Institution shall comply with, the terms and conditions set out in the Controller-Controller Standard Contractual Clauses appended to this Agreement as Appendix VII. In case of discrepancy between the provisions of Appendix VII and any other document included in this Agreement and/or its appendices, the provision included in Appendix VII shall prevail. 2.20 FRCBS or its representative may at any moment inform the User Institution of a Research Participant withdrawing their consent or exercising their rights as a data subject under the GDPR. The User Institution shall perform all actions necessary in order to fulfil the rights of the Research Participant. 2.21 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 Finland and shall be subject to the exclusive jurisdiction of the Finnish courts. 2.22 This Agreement may be executed in counterparts, each and every one of which shall be deemed an original and all of which together shall constitute one and the same instrument. Each party may execute the Agreement in Adobe Portable Document Format (PDF) sent by electronic mail or as otherwise agreed between the parties. PDF signatures of authorised signatories of the parties shall be deemed to be original signatures, shall be valid and binding upon the parties, and, upon delivery, shall constitute due execution of this Agreement.

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
EGAS00001004918	Oxford Nanopore RNA sequencing for HLA typing	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
EGAF00004955672	fastq.gz	11.6 MB
EGAF00004955673	fastq.gz	19.1 MB
EGAF00004955674	fastq.gz	17.9 MB
EGAF00004955675	fastq.gz	34.1 MB
EGAF00004955676	fastq.gz	16.0 MB
EGAF00004955677	fastq.gz	27.4 MB
EGAF00004955678	fastq.gz	27.7 MB
EGAF00004955679	fastq.gz	5.3 MB
EGAF00004955680	fastq.gz	6.6 MB
EGAF00004955681	fastq.gz	22.8 MB
EGAF00004955682	fastq.gz	8.6 MB
EGAF00004955683	fastq.gz	36.3 MB
EGAF00004955684	fastq.gz	18.4 MB
EGAF00004955685	fastq.gz	5.1 MB
EGAF00004955686	fastq.gz	7.2 MB
EGAF00004955687	fastq.gz	12.9 MB
EGAF00004955688	fastq.gz	4.3 MB
EGAF00004955689	fastq.gz	29.9 MB
EGAF00004955690	fastq.gz	8.3 MB
EGAF00004955691	fastq.gz	35.2 MB
EGAF00004955692	fastq.gz	7.3 MB
EGAF00004955693	fastq.gz	20.7 MB
EGAF00004955694	fastq.gz	25.6 MB
EGAF00004955695	fastq.gz	46.3 MB
EGAF00004955696	fastq.gz	18.4 MB
EGAF00004955697	fastq.gz	11.3 MB
EGAF00004955698	fastq.gz	18.7 MB
EGAF00004955699	fastq.gz	10.2 MB
EGAF00004955700	fastq.gz	9.5 MB
EGAF00004955701	fastq.gz	15.0 MB
EGAF00004955702	fastq.gz	5.6 MB
EGAF00004955703	fastq.gz	11.5 MB
EGAF00004955704	fastq.gz	11.0 MB
EGAF00004955705	fastq.gz	47.5 MB
EGAF00004955706	fastq.gz	9.0 MB
EGAF00004955707	fastq.gz	21.3 MB
EGAF00004955708	fastq.gz	72.1 MB
EGAF00004955709	fastq.gz	41.8 MB
EGAF00004955710	fastq.gz	28.3 MB
EGAF00004955711	fastq.gz	15.5 MB
EGAF00004955712	fastq.gz	10.4 MB
EGAF00004955713	fastq.gz	24.5 MB
EGAF00004955714	fastq.gz	49.5 MB
EGAF00004955715	fastq.gz	15.0 MB
EGAF00004955716	fastq.gz	5.7 MB
EGAF00004955717	fastq.gz	12.4 MB
EGAF00004955718	fastq.gz	21.3 MB
EGAF00004955719	fastq.gz	35.6 MB
EGAF00004955720	fastq.gz	11.4 MB
EGAF00004955721	fastq.gz	54.8 MB
EGAF00004955722	fastq.gz	13.2 MB
EGAF00004955723	fastq.gz	30.3 MB
EGAF00004955724	fastq.gz	13.1 MB
EGAF00004955725	fastq.gz	15.9 MB
EGAF00004955726	fastq.gz	19.8 MB
EGAF00004955727	fastq.gz	13.9 MB
EGAF00004955728	fastq.gz	7.1 MB
EGAF00004955729	fastq.gz	8.9 MB
EGAF00004955730	fastq.gz	11.2 MB
EGAF00004955731	fastq.gz	57.1 MB
EGAF00004955732	fastq.gz	14.7 MB
EGAF00004955733	fastq.gz	28.9 MB
EGAF00004955734	fastq.gz	36.5 MB
EGAF00004955735	fastq.gz	13.1 MB
EGAF00004955736	fastq.gz	19.5 MB
EGAF00004955737	fastq.gz	19.7 MB
EGAF00004955738	fastq.gz	6.6 MB
EGAF00004955739	fastq.gz	18.5 MB
EGAF00004955740	fastq.gz	12.8 MB
EGAF00004955741	fastq.gz	17.9 MB
EGAF00004955742	fastq.gz	28.1 MB
EGAF00004955743	fastq.gz	6.0 MB
EGAF00004955744	fastq.gz	22.0 MB
EGAF00004955745	fastq.gz	16.1 MB
EGAF00004955746	fastq.gz	5.1 MB
EGAF00004955747	fastq.gz	8.7 MB
EGAF00004955748	fastq.gz	25.7 MB
EGAF00004955749	fastq.gz	59.1 MB
EGAF00004955750	fastq.gz	25.8 MB
EGAF00004955751	fastq.gz	15.9 MB
EGAF00004955752	fastq.gz	10.9 MB
EGAF00004955753	fastq.gz	5.6 MB
EGAF00004955754	fastq.gz	23.9 MB
EGAF00004955755	fastq.gz	27.6 MB
EGAF00004955756	fastq.gz	44.3 MB
EGAF00004955757	fastq.gz	56.4 MB
EGAF00004955758	fastq.gz	8.5 MB
EGAF00004955759	fastq.gz	22.2 MB
EGAF00004955760	fastq.gz	20.2 MB
EGAF00004955761	fastq.gz	20.1 MB
EGAF00004955762	fastq.gz	26.9 MB
EGAF00004955763	fastq.gz	6.7 MB
EGAF00004955764	fastq.gz	16.3 MB
EGAF00004955765	fastq.gz	12.0 MB
EGAF00004955766	fastq.gz	17.6 MB
EGAF00004955767	fastq.gz	24.8 MB
EGAF00004955768	fastq.gz	26.1 MB
EGAF00004955769	fastq.gz	15.9 MB
EGAF00004955770	fastq.gz	6.7 MB
EGAF00004955771	fastq.gz	61.0 MB
100 Files (2.1 GB)