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Post Mortem brain data used in paper "Significant and pervasive effects of RNA degradation on Nanopore direct RNA sequencing"

This dataset contains data used in the paper titled "Significant and pervasive effects of RNA degradation on Nanopore direct RNA sequencing. The data consists of one post mortem sample that was sequenced with direct RNA sequencing form Oxford Nanopore Technologies on a promethION flow cell.

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Terms and conditions under which data can be accessed.

Date Parties The University of Melbourne ABN 84 002 705 224 a body politic and corporate established in 1853 and constituted under the University of Melbourne Act 2009 (Vic) (University) Party Name of (Recipient) Background A. The University encourages applications from bona fide researchers for access to the Data for participation in new and ongoing research activities. B. This Agreement sets out the terms and conditions where by a Recipient will receive access to the Data for the sole purpose of conducting the Project. Agreed terms 1. Defined terms and interpretation 1.1 Defined terms In this Agreement: Completion Date means: (a) the date detailed in the Schedule 1; or (b) any other date agreed in writing by the parties; Confidential Information means the Data and all information in whatever form relating to inventions, ideas, know-how, concepts, trade secrets, facts, data, processes, discoveries, chemical compositions or formulations, techniques, products, routines, prototypes, specifications, drawings, names, technology methods, computer programs, works in which copyright subsists, other Intellectual Property or the business or financial affairs of a party disclosed or made available in connection with this Agreement; Data means patient genetic data as specified under Item 2 of Schedule 1, which may include DNA microarray, DNA-sequencing and/or RNA-sequencing data. Data Breach means any misuse, interference, loss, unauthorised access, modification or disclosure or any other event or circumstance that may compromise the security or integrity of the Data. Disclosing Party means a party who discloses or makes available Confidential Information. Good Industry Practice means the use of up-to-date and advanced techniques and methodologies having regard to any prevailing international standards and processes, techniques and methodologies used by organisations undertaking human research. Intellectual Property means all rights under statutes, general law or in equity resulting from intellectual activity in the industrial, scientific, literary and artistic fields, including: (c) patents, copyrights, trademarks, company or business names, domain names, semiconductor or circuit layout rights, designs; (d) any rights relating to Confidential Information (including trade secrets) and personal information; and (e) any rights to seek the registration of any of the above rights in Australia or anywhere in the world; Modifications means any improvements, derivatives or modifications arising directly or indirectly from the Recipient’s use of the Data; Personal Information means information or an opinion (including information or an opinion forming part of a database), whether true or not, and whether recorded in writing or spoken form, about an individual whose identity is apparent, or can reasonably be ascertained, from the information or opinion. Project means a research project which has received Recipient’s Human Research Ethics Committee approval and as further defined in Schedule 1; Publication means the publication of an abstract, article, manuscript or paper, presentation at a conference or seminar, or other public disclosure, where such publication specifically discloses (wholly or partly) the actual Project outputs, including any Project Intellectual Property and Publish is to be similarly construed Research Participant means an individual whose data form part of these Data. Receiving Party means a party to whom Confidential Information is disclosed or made available. Recipient has the meaning as defined in Schedule 1. Responsible Investigator has the meaning as defined in Schedule 1. 1.2 Interpretation In this Agreement, unless the context requires otherwise: (a) the singular includes the plural and vice versa and a reference to any gender includes all genders; (b) if a word or phrase is defined, its other grammatical forms have the corresponding meaning; (c) any reference to: (i) this Agreement means this document, including any schedules or annexures, as varied, novated or replaced from time to time; (ii) a clause, paragraph, schedule, attachment or annexure is a reference to this Agreement, and a reference to this Agreement includes any schedule, attachment or annexure; (iii) a document or instrument includes the document or instrument as novated, altered, supplemented or replaced from time to time; (iv) a reference to time is to time in Melbourne, Australia; (v) a party includes its agents, employees, invitees, officers, permitted successors, transferees and assigns; (vi) “writing” includes electronic transmission and any means of reproducing words in a tangible and permanently visible form; (vii) a person includes a natural person, partnership, body corporate, association, governmental or local authority or agency or other entity; (viii) a legislation, statute, ordinance, code or other law includes regulations and other instruments under it and consolidations, amendments, re-enactments or replacements; (d) headings are for convenience only and do not affect interpretation; (e) if a day on or by which an obligation must be performed or an event must occur is not a Business Day, the obligation must be performed or the event must occur on or by the next Business Day; (f) any word of limitation such as ‘including’ and any other similar expression, is to be read with the words ‘but not limited to’ immediately after; and (g) no rule of construction will apply to a clause to the disadvantage of a party merely because that party proposed the clause or would otherwise benefit from it. 2. Use of the Data (a) The Recipient must: (i) use the Data only for the Project and not for any other purpose; (ii) may not use the Data for a commercial purpose; (iii) not to link or combine the Data to other information or archived data available in a way that could re-identify the participants (the subject of the Data), even if access to that data has been formally granted to the Recipient or is freely available without restriction; (iv) not make Intellectual Property claims on the Data and not use Intellectual Property protection in ways that would prevent or block access to, or use of, any element of the Data, or conclusion drawn directly from these Data; (v) 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; (vi) notify the University as soon as it becomes aware of a breach of the terms or conditions of this Agreement; (vii) complete the Project Brief detailed in Schedule 1. (viii) not distribute the Data to any third party without the University’s prior written consent; and (ix) store, handle and use the Data in compliance with all applicable laws. (b) Without limiting the provisions of this clause 2, the Recipient agrees: (i) to comply with the Privacy Act 1988 (Cth) and the requirements of Division 2 of Part III of that Act and the Health Records Act 2001 (Vic) and the health privacy principles set out in schedule 1 of that Act in the use, collection, storage and security or disclosure of any personal and/or health information collected or used for the Project and, if the context so permits, any other applicable legislation, industry codes or policies relating to handling or protecting personal or health information and related ethical issues. (ii) 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. (iii) 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; (iv) not re-identify or attempt to re-identify any Data; (v) implement and comply with appropriate technical and organisational measures to ensure the security of the Data, which must include measures aimed at preventing the loss of, damage to, and unauthorised access to or use of the Data. Such measures must be at least to the standard that you would implement and comply with for the security of your own confidential data, which in any event must comply with Good Industry Practice; (vi) notify the University immediately (and in any event no later than three (3) Business days) after: (A) becoming aware of any actual or suspected Data Breach or any suspected inaccuracy in any Data; or (B) you inadvertently re-identify any component of Data or otherwise detect any Personal Information; and in any such notification you must provide the University with a reasonably detailed description of the relevant circumstances; (vii) comply with: (A) your own data security policies and procedures; (B) the Privacy Act 1988 (Cth), the Privacy and Data Protection Act 2014 (Vic) and the Health Records Act 2001 (Vic) to the extent applicable to the Approved Research and your receipt of the Data; and (C) if the Approved Research is not based in Australia, the local privacy and personal and health information handling laws and regulations. (c) The Recipient must at all times, during when the Data is in its possession, ensure that it engage someone to act as its key person responsible for managing access, use and security of the Data (“Data Custodian”). 3. Intellectual Property in Data and Results (a) The University retains all ownership and Intellectual Property Rights in the Data. (b) The University grants the Recipient a non-exclusive, royalty-free licence to use, adapt, reproduce and exploit the Data for the Project; (c) In consideration of the University supplying the Data to the Recipient, the Recipient will, as soon as practicable, inform the University in writing of any and all findings or information it has derived from the Data (Results) and of any new Intellectual Property Rights developed from its use of the Data. The Recipient and the University will enter into negotiations to discuss their respective ownership rights in relation to any new Intellectual Property Rights in the Results. 4. Publication (a) The Recipient shall not publish or publicly disclose any Confidential Information of the University, the Data or Results without first obtaining the prior written consent of the University (such consent not to be unreasonably withheld). (b) The Recipient must acknowledge the University’s contribution in any Publication in accordance with the Australian Code for the Responsible Conduct of Research. (c) The Recipient must describe how the Data can be accessed, including the name of the hosting database and its accession numbers in any Publication. 5. No Warranty The Recipient acknowledges that: (a) the University makes no representations and extends no warranties of any kind, either express or implied, including in relation to merchantability or fitness for a particular purpose or that the use of the Data will not infringe any Intellectual Property rights; (b) the Recipient stores, handles and uses the Data at its own risk; and (c) unless prohibited by law, the Recipient assumes liability for all claims against the University by third parties which may arise from the Recipient’s use, storage or disposal of the Data. 6. Indemnity The Recipient indemnifies, and keeps indemnified, the University and its officers, employees and agents from and against all loss suffered or incurred by, and any claim against, the University arising out of or in connection with the Recipient's: (a) storage, handling or use of the Data, Modifications or Confidential Information; or (b) breach of this Agreement. 7. Confidentiality (a) The Receiving Party will: (i) keep all Confidential Information of the Disclosing Party strictly confidential, unless clause 7(a)(v) applies; (ii) limit access to those of its personnel reasonably requiring the Confidential Information for the Project on a strictly need to know basis; (iii) not use the Confidential Information in any way other than for the Project or as otherwise contemplated by this Agreement without the prior written permission of the Disclosing Party; (iv) ensure that all personnel within the Recipient’s organisation (including researchers working on the Project) to whom the Confidential Information is disclosed are bound to keep the Confidential Information confidential and not to use the Confidential Information except for the Project; and (v) to the extent legally permitted to do so, immediately notify the Disclosing Party of any disclosure required by law and, before making any such disclosure, provide the Disclosing Party with a reasonable opportunity to minimise the extent of such disclosure, including challenging the requirement or obtaining an order or ruling to preserve confidentiality. (b) Return or Destruction of Confidential Information (i) At any time upon the written request of the Disclosing Party, the Receiving Party will, at its own expense, promptly destroy or return to the Disclosing Party (at Disclosing Party’s option) any documents which embody the Disclosing Party’s Confidential Information. (ii) The above clause does not prevent the Recipient from retaining a copy of the Confidential Information solely for archival purpose in conformity with audit or legal requirements. 8. Termination (a) The University may terminate this agreement at any time with immediate effect by giving written notice to the Recipient. (b) Any obligations in relation to confidentiality and privacy under this Agreement continue to apply to the parties to this Agreement after termination. (c) Termination of this Agreement does not affect any accrued rights or remedies that the University may have. (d) Notwithstanding any other provision of this agreement, upon termination of this agreement for any reason, or abandonment of the Project, the Recipient must destroy/discard all copies of the Data in its possession or control. This clause does not prevent the Recipient from retaining a copy of the Data solely for archival purpose in conformity with audit or legal requirements. 9. Notices. (a) Notices must be in writing and signed by a duly authorised person. (b) Notices must be sent to the party’s address specified in the “Parties” section of this Agreement in respect of that party. (c) Notices to or by a party are deemed to be given by the sender and received by the addressee as follows: (i) if by hand, when delivered to the addressee; (ii) if by domestic post, 4 Business Days from and including the date of postage; (iii) if by international post, 10 Business Days from and including the date of postage; (iv) if by email, when an emailed notice is acknowledged by the recipient personally (that is, not by any automatically generated system email); or (v) or if by facsimile, when transmitted to the addressee, provided that if by electronic transmission on a day which is not, or is after 5.00pm (addressee’s time) on, a Business Day, then on the next Business Day. 10. General (a) This Agreement is governed by the laws of the State of Victoria, Australia. The parties submit to the jurisdiction of the courts of the State of Victoria and any courts which may hear appeals from those courts. (b) This Agreement constitutes the entire agreement of the parties with respect to its subject matter and supersedes all prior oral or written representations and agreements. (c) The Recipient accepts that it may be necessary for the University to alter the terms of this Agreement from time to time. In the event that changes are required, the University will contact the Recipient to inform it of the changes and the Recipient may elect to accept the changes or terminate the Agreement. (d) Subject to amendments permitted under clause 10(c), the agreement may otherwise only be amended in writing signed by the parties. (e) The parties are independent contracting parties. Nothing in this Agreement will make any party the agent, partner or legal representative of the other party. (f) This Agreement may be executed in counterparts, each of which will be an original (and any electronic copy of the same will be deemed to be an original) and all executed counterparts will be taken together to constitute one document.   Schedule 1 – Project Brief Item 1 Project Description/Purpose (“Project”) Item 2 Data Item 3 Recipient Details Item 4 Head of Department Item 5 Responsible Investigator(s) Item 6 Evidence that the Project has been approved by Recipient’s Human Research Ethics Committee Item 7 Project Time Period Item 8 Project Significance Item 9 Completion Date   Signing Page Executed as an Agreement Signed for and on behalf of The University of Melbourne in the presence of: Signature of Authorised Person Signature of Witness Name of Authorised Person (print) Name of Witness (print) Date Signed for and on behalf of the Recipient in the presence of: Signature of Director / Authorised Officer Signature of Witness Name of Director / Authorised Officer (please print) Name of Witness (please print) Date

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
EGAS00001006542 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
EGAF00006924101 fastq.gz 8.8 GB
1 File (8.8 GB)