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RNA-seq of oropharynx cancer cases from University of Michigan

This dataset consists of 67 bulk RNA-seq data (sorted aligned BAM files) from formalin-fixed paraffin-embedded (FFPE) oropharynx tumor samples from the University of Michigan (UM). Samples were collected as part of the UM Head and Neck SPORE between 2008-2014. Library preparation was performed using the ribo-depletion method with the FastSelect kit and sequenced on the NovaSeq 6000 at the UM Advanced Genomics Core, resulting in 150bp paired-end reads. Raw reads were trimmed using Cutadapt (v3.4) and aligned to hg38 and high-risk HPV genomes using STAR (v2.7.9a). 62 of 67 samples were determined to be HPV RNA-positive.

Request Access

DUO:0000015
version: 2021-02-23

no general methods research

This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms).

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.

Michigan-Georgetown Cancer EGA Policy

Data Access Agreement Non-Identifying Data Use and Confidentiality Agreement This Data Access Agreement (the “Agreement”) explains the terms for which access will be granted to the data generated by the Michigan-Georgetown Cancer investigators, i.e. Drs. Laura Rozek, Maureen Sartor, and Nisha D’Silva. It is entered into by and between the above investigators, currently at University of Michigan and/or Georgetown University (“Provider”) and a researcher whose institution has previously completed this Data Access Agreement and has received acknowledgement of its acceptance (“Data User”). 1. Definitions: The parties agree that the following terms, when used in this Agreement, shall have the following meanings, and that the terms set forth below shall be deemed to be modified to reflect any changes made hereafter to such terms by law or regulation. • "Confidential Information" means any and all information and data, which is not publicly known, and which is disclosed to the Data User by the Provider, subject to the terms of this Agreement. • “Data Set” means any and all data obtained from the Provider (typically human genomic data). 2. Terms and Obligations of Data User: • Performance of Activities. Data User may use and disclose the Data Set only for the advancement of medical research, and according to the consent obtained from sample donors and as permitted by this Agreement. Data User will not re-identify the data or contact the Data participants who have given their informed consent. • Permitted Access to Data Set. Data User shall limit the use of the Data Set to the approved individuals or classes of individuals who need the Data Set for the performance of the approved purpose and project described in the Data User’s application. Use of the Data Set for a new purpose or project will require a new application and approval. • Assurances of Data User’s Non-Employee Agents. Data User shall not disclose the Data Set to any non-employee agent or subcontractor of Data User except with the prior written consent of the Provider. Data User shall ensure that any agents, including subcontractors, to whom it provides the Data Set agree in writing to be bound by the same restrictions and conditions that apply to Data User with respect to such Data Set. • Safeguards. Data User must have a locally approved Institutional Review Board (IRB) to oversee appropriate use of the Data Set, and use appropriate safeguards to prevent use or disclosure of the Data Set other than as provided by this Agreement. 3. Confidential Information: • Purpose. The parties agree that Provider’s disclosures of Confidential Information to Data User are for the sole purpose of Data User’s research. • Exceptions. The Data User shall not be liable for the disclosure or use of Provider’s Confidential Information that the Data User can demonstrate by competent physical evidence: i) was known to the Data User prior to the disclosure by the Provider; or ii) is or becomes publicly known through no fault or omission attributable to the Data User; or iii) is rightfully given to the Data User by a third party under no obligation of confidentiality to the Provider; or iv) is independently developed by the Data User without the aid, application or use of such Confidential Information; or v) is required to be disclosed by law, governmental regulation or order of a court of competent jurisdiction; or vi) is disclosed pursuant to prior and specific written consent of the Provider. • Legal or Administrative Proceeding. In the event Data User is required to disclose Provider’s Confidential Information pursuant to this agreement, Data User agrees to give Provider reasonably advance written notice of its required disclosure. Provider, in its sole discretion and expense, may then seek a protective order or other remedy and/or waive compliance with the provisions of this Agreement. To the extent permitted by law, Data User will assist and cooperate in good faith with Provider, at Provider’s expense. In the event that such protective order or other remedy is not obtained or sought by Provider, Data User will: (i) disclose only that portion of the Confidential Information that is legally required to be disclosed in the opinion of Data User’s legal counsel, (ii) take such steps as are reasonably necessary not to prejudice the parties’ right to protect such Confidential Information and (iii) request the requiring adjudicating body and/or agency to maintain the confidentiality of such Confidential Information. Employees; Third Parties. The Data User will disclose the Provider’s Confidential Information only to those employees, agents, representatives, consultants and/or subcontractors who have a reasonable need-to-know as a part of the Data User’s evaluation of such for the research development described in the Data User’s application and shall exercise no less than reasonable care in holding such information in confidence pursuant to the terms of this Agreement and. The Data User shall require its respective employees, agents, representatives, consultants and subcontractors described herein to comply with the terms of this Agreement. Any publication must be provided to Provider sixty (60) days in advance for review to confirm that it meets the terms of this Agreement and the approved purpose and project described in the Data User’s application. • Prohibited Use. The Data User further agrees to not: (1) copy, reproduce or otherwise reduce to writing any part of the Provider’s Confidential Information except and only as may be reasonably necessary for the purpose described herein, and that all Confidential Information, including any materials or media that contain the Confidential Information and all copies thereof, shall remain the exclusive property of the Provider, and (2) make any commercial use of any of Provider’s Confidential Information, in whole or in part, without the Provider’s prior written and specific consent. Notwithstanding, nothing in this Agreement shall be construed to limit the Data User from independently developing, selling or acquiring knowledge, information, services or products of any kind without the use of the Provider’s Confidential Information. • Warranty. No Obligation to receive Confidential Information. Provider warrants that it has the right to disclose the Confidential Information actually disclosed under this Agreement. Nothing in this Agreement shall be construed to impose any obligation on the Data User to receive any Confidential Information that it does not wish to receive, or to enter into any other agreement of any nature, nor shall this Agreement result in any claim whatsoever by one party against another for reimbursement of costs for any effort expended. This Agreement is for protecting Confidential Information only. • Notices. All notices concerning this Agreement shall be in writing and deemed sufficiently given if delivered in person with a receipt signed by the person accepting delivery; or sent by facsimile or electronic mail; or by registered or certified mail, postage prepaid; or by recognized overnight delivery service; each with confirmation of receipt, to the Provider as specified by the relevant signature line below. • No Public Disclosures. No party shall issue any public disclosures or statements regarding this Agreement or the subject matter thereof without the prior written consent of the other party. •Injunctive Relief. The Data User acknowledges that the Provider may not have an adequate remedy at law in the event of any breach or threatened breach by Data User of any provision of this Agreement and that the Provider would likely suffer irreparable damage and injury as a result. Accordingly, in the event of any such breach or threatened breach, Data User hereby agrees that Provider shall be entitled to seek immediate injunctive relief without the posting by the Provider of any bond or other security therefore, and Data User further agrees not to raise as a defense the availability of monetary damages as a remedy. 4. Material Breach, Enforcement and Termination: • Term. This Agreement shall remain in force for a period of one (1) year, unless earlier terminated upon thirty (30) days written notice by the terminating party, as evidenced by a confirmation of receipt. The obligations of the parties under this Agreement with respect to any Confidential Information shall survive the termination of this Agreement and remain in effect for three (3) years from the date of expiration or earlier termination of this Agreement. 5. Miscellaneous Terms: • Primacy. To the extent that any provisions of this Agreement conflict with the provisions of any other agreement or understanding between the parties, this Agreement shall control. • Data User will accept that Data Set may be reissued from time to time, with suitable versioning. If the reissue is at the request of sample donors and/or other ethical scrutiny, Data User will destroy earlier versions of the Data Set. • Data User will accept that the Provider, the original data creators, depositors or copyright holders, or the funders of the Data Set or any part of the data supplied: (1) bear no legal responsibility for the accuracy or comprehensiveness of the Data; and (2) accept no liability for indirect, consequential, or incidental, damages or losses arising from use of the Data Set, or from the unavailability of, or break in access to, the Data Set for whatever reason. • Data User will acknowledge use of this Data Set in any resulting publications using the following wording: “This study makes use of data generated by the investigators of the Michigan-Georgetown Cancer collaboration at University of Michigan and Georgetown University. Funding support was provided by the University of Michigan Rogel Cancer Center and Georgetown University Lombardi Comprehensive Cancer Center”. • Drs. Maureen Sartor, Laura Rozek, and Nisha D’Silva will have an opportunity to review any publications that result from the dataset. Data Recipient should be aware that the Consortium bears no responsibility for the further analysis or interpretation of these data, over and above that published by the Michigan-Georgetown Cancer investigators. AGREED FOR USER INSTITUTION ("Data User") By: ______________________ Title: ______________________ Date: ______________________ ASSURANCE OF COMPLIANCE WITH DATA ACCESS AGREEMENT The following individuals are authorized to receive and use the Data Set described in the Data Access Agreement for the purposes described above. By signing below, we acknowledge the restrictions on our use and disclosure of the Data Set in accordance with the Agreement. Name of Applicant(s): ________________________________________ ________________________________________ ________________________________________ ________________________________________ Signature of Applicant(s): ________________________________________ ________________________________________ ________________________________________ ________________________________________ Date: ______________________ For and on behalf of User Institution: Signature of Institutional or Administrative Authority: ________________________________________ Print name: ________________________________________ User Institution: ___________________________________ Date: _______________________________ WHEN SUBMITTING THIS DOCUMENT, PLEASE INCLUDE ALL PAGES OF THE AGREEMENT WITH THIS SIGNATURE PAGE

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
EGAS50000000893 RNASeq

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
EGAF50000321585 bam 9.6 GB
EGAF50000321586 bam 8.1 GB
EGAF50000321587 bam 8.2 GB
EGAF50000321588 bam 5.5 GB
EGAF50000321589 bam 6.5 GB
EGAF50000321590 bam 13.3 GB
EGAF50000321591 bam 5.3 GB
EGAF50000321592 bam 8.0 GB
EGAF50000321593 bam 6.3 GB
EGAF50000321594 bam 9.8 GB
EGAF50000321595 bam 9.1 GB
EGAF50000321596 bam 8.5 GB
EGAF50000321597 bam 9.9 GB
EGAF50000321598 bam 5.2 GB
EGAF50000321599 bam 11.7 GB
EGAF50000321600 bam 8.9 GB
EGAF50000321601 bam 8.3 GB
EGAF50000321602 bam 7.7 GB
EGAF50000321603 bam 9.3 GB
EGAF50000321604 bam 12.0 GB
EGAF50000321605 bam 11.3 GB
EGAF50000321606 bam 5.2 GB
EGAF50000321607 bam 8.1 GB
EGAF50000321608 bam 9.5 GB
EGAF50000321609 bam 8.1 GB
EGAF50000321610 bam 12.7 GB
EGAF50000321611 bam 9.3 GB
EGAF50000321612 bam 7.2 GB
EGAF50000321613 bam 8.9 GB
EGAF50000321614 bam 10.9 GB
EGAF50000321615 bam 7.6 GB
EGAF50000321616 bam 7.9 GB
EGAF50000321617 bam 9.2 GB
EGAF50000321618 bam 10.5 GB
EGAF50000321619 bam 7.4 GB
EGAF50000321620 bam 6.5 GB
EGAF50000321621 bam 9.5 GB
EGAF50000321622 bam 10.4 GB
EGAF50000321623 bam 11.3 GB
EGAF50000321624 bam 9.7 GB
EGAF50000321625 bam 4.7 GB
EGAF50000321626 bam 7.0 GB
EGAF50000321627 bam 9.2 GB
EGAF50000321628 bam 8.6 GB
EGAF50000321629 bam 7.2 GB
EGAF50000321630 bam 10.0 GB
EGAF50000321631 bam 8.6 GB
EGAF50000321632 bam 9.7 GB
EGAF50000321633 bam 9.5 GB
EGAF50000321634 bam 14.2 GB
EGAF50000321635 bam 18.3 GB
EGAF50000321636 bam 11.5 GB
EGAF50000321637 bam 18.3 GB
EGAF50000321638 bam 9.3 GB
EGAF50000321639 bam 11.6 GB
EGAF50000321640 bam 9.1 GB
EGAF50000321641 bam 12.5 GB
EGAF50000321642 bam 8.1 GB
EGAF50000321643 bam 8.0 GB
EGAF50000321644 bam 8.3 GB
EGAF50000321645 bam 9.3 GB
EGAF50000321646 bam 10.4 GB
EGAF50000321647 bam 9.0 GB
EGAF50000321648 bam 8.2 GB
EGAF50000321649 bam 9.3 GB
EGAF50000321650 bam 8.9 GB
EGAF50000321651 bam 11.4 GB
67 Files (622.6 GB)