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UIC HNSCC RNA-Seq and miRNA-Seq Data

This dataset contains matched RNA-Seq and miRNA-Seq fastq files from 109 match samples of 34 human Papillomavirus-negative Head and Neck cancer patients, including 72 lymph nodes, 29 tumor and 8 normal samples.

Request Access

These terms and conditions govern access to the managed access dataset (EGAS00001003233) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions.

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 Authorized Personnel: The individuals at the User Institution to whom UIC-HNSCC 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 Producers: UIC-HNSCC 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. XXXXX: Your Institution details here 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 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. 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 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. 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 UIC-HNSCC within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify UIC-HNSCC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify UIC-HNSCC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. UIC-HNSCC 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 UIC-HNSCC. 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 United States of American and shall be subject to the exclusive jurisdiction of the US courts. 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 UIC-HNSCC Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) EGAS00001003233 Name of project that created the dataset Molecular Classification of Head and Neck Cancer Lymph Node Metastases Subtypes 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 screenlocks (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 APPENDIX III – PUBLICATION POLICY UIC-HNSCC intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. UIC-HNSCC anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until 3 months after these data were first made available on the relevant hosting database, unless UIC-HNSCC has provided written consent to earlier submission. 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., EGAS00001003233), and acknowledge its use in a form agreed by the User Institution with UIC-HNSCC.

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
Transcriptome Analysis

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
EGAF00002248603 fastq.gz 347.5 MB
EGAF00002258411 fastq.gz 1.1 GB
EGAF00002258412 fastq.gz 275.6 MB
EGAF00002258413 fastq.gz 319.1 MB
EGAF00002258414 fastq.gz 364.4 MB
EGAF00002258415 fastq.gz 372.9 MB
EGAF00002258416 fastq.gz 1.5 GB
EGAF00002258417 fastq.gz 1.4 GB
EGAF00002258418 fastq.gz 218.1 MB
EGAF00002258419 fastq.gz 220.5 MB
EGAF00002258420 fastq.gz 1.5 GB
EGAF00002258421 fastq.gz 1.3 GB
EGAF00002258422 fastq.gz 2.7 GB
EGAF00002258423 fastq.gz 202.1 MB
EGAF00002258424 fastq.gz 197.1 MB
EGAF00002258425 fastq.gz 1.4 GB
EGAF00002258426 fastq.gz 1.4 GB
EGAF00002258427 fastq.gz 1.4 GB
EGAF00002258428 fastq.gz 1.7 GB
EGAF00002258429 fastq.gz 1.9 GB
EGAF00002258430 fastq.gz 1.5 GB
EGAF00002258431 fastq.gz 1.5 GB
EGAF00002258432 fastq.gz 294.6 MB
EGAF00002258433 fastq.gz 232.3 MB
EGAF00002258434 fastq.gz 1.5 GB
EGAF00002258435 fastq.gz 1.7 GB
EGAF00002258436 fastq.gz 431.1 MB
EGAF00002258437 fastq.gz 258.4 MB
EGAF00002258438 fastq.gz 268.6 MB
EGAF00002258439 fastq.gz 536.1 MB
EGAF00002258440 fastq.gz 1.7 GB
EGAF00002258441 fastq.gz 1.7 GB
EGAF00002258442 fastq.gz 1.7 GB
EGAF00002258443 fastq.gz 1.4 GB
EGAF00002258444 fastq.gz 240.0 MB
EGAF00002258445 fastq.gz 481.8 MB
EGAF00002258446 fastq.gz 1.9 GB
EGAF00002258447 fastq.gz 263.0 MB
EGAF00002258448 fastq.gz 339.0 MB
EGAF00002258449 fastq.gz 2.0 GB
EGAF00002258450 fastq.gz 324.4 MB
EGAF00002258451 fastq.gz 235.8 MB
EGAF00002258452 fastq.gz 202.3 MB
EGAF00002258453 fastq.gz 1.7 GB
EGAF00002258454 fastq.gz 1.5 GB
EGAF00002258455 fastq.gz 360.2 MB
EGAF00002258456 fastq.gz 383.4 MB
EGAF00002258457 fastq.gz 1.5 GB
EGAF00002258458 fastq.gz 2.0 GB
EGAF00002258459 fastq.gz 286.5 MB
EGAF00002258460 fastq.gz 209.8 MB
EGAF00002258461 fastq.gz 1.2 GB
EGAF00002258462 fastq.gz 1.7 GB
EGAF00002258463 fastq.gz 1.7 GB
EGAF00002258464 fastq.gz 3.3 GB
EGAF00002258465 fastq.gz 1.8 GB
EGAF00002258466 fastq.gz 1.2 GB
EGAF00002258467 fastq.gz 1.5 GB
EGAF00002258468 fastq.gz 1.9 GB
EGAF00002258469 fastq.gz 1.7 GB
EGAF00002258470 fastq.gz 1.8 GB
EGAF00002258471 fastq.gz 191.0 MB
EGAF00002258472 fastq.gz 400.7 MB
EGAF00002258473 fastq.gz 210.9 MB
EGAF00002258474 fastq.gz 357.9 MB
EGAF00002258475 fastq.gz 473.4 MB
EGAF00002258476 fastq.gz 239.7 MB
EGAF00002258477 fastq.gz 214.0 MB
EGAF00002258478 fastq.gz 405.6 MB
EGAF00002258479 fastq.gz 378.1 MB
EGAF00002258480 fastq.gz 684.8 MB
EGAF00002258481 fastq.gz 239.5 MB
EGAF00002258482 fastq.gz 332.4 MB
EGAF00002258483 fastq.gz 961.5 MB
EGAF00002258484 fastq.gz 243.3 MB
EGAF00002258485 fastq.gz 236.2 MB
EGAF00002258486 fastq.gz 196.2 MB
EGAF00002258487 fastq.gz 228.0 MB
EGAF00002258488 fastq.gz 1.8 GB
EGAF00002258489 fastq.gz 1.9 GB
EGAF00002258490 fastq.gz 2.0 GB
EGAF00002258491 fastq.gz 1.8 GB
EGAF00002258492 fastq.gz 2.2 GB
EGAF00002258493 fastq.gz 1.4 GB
EGAF00002258494 fastq.gz 1.3 GB
EGAF00002258495 fastq.gz 1.0 GB
EGAF00002258496 fastq.gz 1.4 GB
EGAF00002258497 fastq.gz 1.7 GB
EGAF00002258498 fastq.gz 1.6 GB
EGAF00002258499 fastq.gz 2.2 GB
EGAF00002258500 fastq.gz 1.3 GB
EGAF00002258501 fastq.gz 1.1 GB
EGAF00002258502 fastq.gz 355.6 MB
EGAF00002258503 fastq.gz 373.1 MB
EGAF00002258504 fastq.gz 1.6 GB
EGAF00002258505 fastq.gz 1.7 GB
EGAF00002258506 fastq.gz 1.6 GB
EGAF00002258507 fastq.gz 2.2 GB
EGAF00002258508 fastq.gz 1.3 GB
EGAF00002258509 fastq.gz 1.4 GB
EGAF00002258510 fastq.gz 1.4 GB
EGAF00002258511 fastq.gz 1.5 GB
EGAF00002258512 fastq.gz 224.3 MB
EGAF00002258513 fastq.gz 276.1 MB
EGAF00002258514 fastq.gz 428.8 MB
EGAF00002258515 fastq.gz 260.9 MB
EGAF00002258516 fastq.gz 234.2 MB
EGAF00002258517 fastq.gz 234.3 MB
EGAF00002258518 fastq.gz 402.5 MB
EGAF00002258519 fastq.gz 542.0 MB
EGAF00002258520 fastq.gz 1.0 GB
EGAF00002258521 fastq.gz 191.4 MB
EGAF00002258522 fastq.gz 330.9 MB
EGAF00002258523 fastq.gz 1.8 GB
EGAF00002258524 fastq.gz 1.4 GB
EGAF00002258525 fastq.gz 1.9 GB
EGAF00002258526 fastq.gz 250.2 MB
EGAF00002258527 fastq.gz 1.3 GB
EGAF00002258528 fastq.gz 1.5 GB
EGAF00002258529 fastq.gz 1.4 GB
EGAF00002258530 fastq.gz 449.6 MB
EGAF00002258531 fastq.gz 213.5 MB
EGAF00002258532 fastq.gz 375.2 MB
EGAF00002258533 fastq.gz 358.4 MB
EGAF00002258534 fastq.gz 397.5 MB
EGAF00002258535 fastq.gz 242.8 MB
EGAF00002258536 fastq.gz 1.5 GB
EGAF00002258537 fastq.gz 209.1 MB
EGAF00002258538 fastq.gz 1.6 GB
EGAF00002258539 fastq.gz 320.3 MB
EGAF00002258540 fastq.gz 1.8 GB
EGAF00002258541 fastq.gz 1.9 GB
EGAF00002258542 fastq.gz 219.4 MB
EGAF00002258543 fastq.gz 1.7 GB
EGAF00002258544 fastq.gz 2.0 GB
EGAF00002258545 fastq.gz 1.8 GB
EGAF00002258546 fastq.gz 2.4 GB
EGAF00002258547 fastq.gz 314.9 MB
EGAF00002258548 fastq.gz 1.8 GB
EGAF00002258549 fastq.gz 1.7 GB
EGAF00002258550 fastq.gz 1.6 GB
EGAF00002258551 fastq.gz 1.3 GB
EGAF00002258552 fastq.gz 1.4 GB
EGAF00002258553 fastq.gz 311.6 MB
EGAF00002258554 fastq.gz 1.4 GB
EGAF00002258555 fastq.gz 424.3 MB
EGAF00002258556 fastq.gz 196.9 MB
EGAF00002258557 fastq.gz 398.3 MB
EGAF00002258558 fastq.gz 759.3 MB
EGAF00002258559 fastq.gz 250.0 MB
EGAF00002258560 fastq.gz 1.8 GB
EGAF00002258561 fastq.gz 1.4 GB
EGAF00002258562 fastq.gz 1.3 GB
EGAF00002258563 fastq.gz 208.2 MB
EGAF00002258564 fastq.gz 196.9 MB
EGAF00002258565 fastq.gz 1.8 GB
EGAF00002258566 fastq.gz 2.7 GB
EGAF00002258567 fastq.gz 1.6 GB
EGAF00002258568 fastq.gz 1.5 GB
EGAF00002258569 fastq.gz 1.7 GB
EGAF00002258570 fastq.gz 382.7 MB
EGAF00002258571 fastq.gz 356.9 MB
EGAF00002258572 fastq.gz 1.7 GB
EGAF00002258573 fastq.gz 330.7 MB
EGAF00002258574 fastq.gz 252.7 MB
EGAF00002258575 fastq.gz 1.7 GB
EGAF00002258576 fastq.gz 1.6 GB
EGAF00002258577 fastq.gz 1.8 GB
EGAF00002258578 fastq.gz 339.9 MB
EGAF00002258579 fastq.gz 2.1 GB
EGAF00002258580 fastq.gz 2.1 GB
EGAF00002258581 fastq.gz 391.1 MB
EGAF00002258582 fastq.gz 2.0 GB
EGAF00002258583 fastq.gz 270.2 MB
EGAF00002258584 fastq.gz 1.6 GB
EGAF00002258585 fastq.gz 1.9 GB
EGAF00002258586 fastq.gz 292.2 MB
EGAF00002258587 fastq.gz 292.9 MB
EGAF00002258588 fastq.gz 219.0 MB
EGAF00002258589 fastq.gz 323.7 MB
EGAF00002258590 fastq.gz 1.5 GB
EGAF00002258591 fastq.gz 1.7 GB
EGAF00002258592 fastq.gz 2.0 GB
EGAF00002258593 fastq.gz 1.7 GB
EGAF00002258594 fastq.gz 1.2 GB
EGAF00002258595 fastq.gz 1.6 GB
EGAF00002258596 fastq.gz 1.3 GB
EGAF00002258597 fastq.gz 1.3 GB
EGAF00002258598 fastq.gz 1.4 GB
EGAF00002258599 fastq.gz 2.4 GB
EGAF00002258600 fastq.gz 1.8 GB
EGAF00002258601 fastq.gz 1.1 GB
EGAF00002258602 fastq.gz 1.0 GB
EGAF00002258603 fastq.gz 359.4 MB
EGAF00002258604 fastq.gz 344.2 MB
EGAF00002258605 fastq.gz 580.4 MB
EGAF00002258606 fastq.gz 293.9 MB
EGAF00002258607 fastq.gz 228.5 MB
EGAF00002258608 fastq.gz 242.6 MB
EGAF00002258609 fastq.gz 340.5 MB
EGAF00002258610 fastq.gz 373.4 MB
EGAF00002258611 fastq.gz 197.9 MB
EGAF00002258612 fastq.gz 215.3 MB
EGAF00002258613 fastq.gz 415.7 MB
EGAF00002258614 fastq.gz 219.6 MB
EGAF00002258615 fastq.gz 227.7 MB
EGAF00002258616 fastq.gz 385.2 MB
EGAF00002258617 fastq.gz 265.8 MB
EGAF00002258618 fastq.gz 585.0 MB
EGAF00002258619 fastq.gz 269.1 MB
EGAF00002258620 fastq.gz 312.8 MB
EGAF00002258621 fastq.gz 441.6 MB
EGAF00002258622 fastq.gz 1.5 GB
EGAF00002258623 fastq.gz 501.4 MB
EGAF00002258624 fastq.gz 360.2 MB
EGAF00002258625 fastq.gz 434.7 MB
EGAF00002258626 fastq.gz 569.4 MB
EGAF00002258627 fastq.gz 604.5 MB
218 Files (215.9 GB)