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Small molecule screen reveals synergy of cell cycle checkpoint kinase inhibitors with DNA-damaging chemotherapies in medulloblastoma (methylation dataset)

human medulloblastoma xenograft isolated from mouse brain was frozen and genomic DNA or RNA was extracted. Bisulfite converted DNA was processed and hybridised to illumina EPIC or 450K arrays using standard protocols. RNAseq was performed on total RNA.

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Access to Data 1. General principles The Telethon Kids Institute (hereafter referred to as Telethon Kids) Brain Tumour Research Program Data Access Committee will consider applications for access to de‐identified molecular genetics data generated from studies based at The Institute. Access to data will be granted to qualified researchers for appropriate health‐related uses. A qualified researcher refers to a scientist who is employed, or a student enrolled at, or legitimately affiliated with an academic, non‐profit or government institution. The data is deposited in the European Genome‐phenome Archive (EGA) and access is by application to the Telethon Kids Institute Brain Tumour Research Program Data Access Committee (TKI-BTRP_DAC). Access to data will be granted to researchers for appropriate use and will be governed by the provisions laid out in the associated informed consent for each cohort or collection, and the terms contained in the Data Access Agreement. The TKI-BTRP_DAC is concerned only with access to the core, de‐identified, data generated by each study. The only phenotypic information held by the TKI-BTRP_DAC is that which is implied by membership of a particular trait or disorder under investigation, case or control group as entered in the EGA repository and associated publications. Data will be accompanied by information on the sex, age and phenotype associated with each sample. The Committee will not consider requests for more detailed demographic or phenotypic information. Access is conditional upon availability of data and signed agreement by the researcher(s) and the responsible employing Institution to abide by policies related to publication, data disposal, ethical approval and confidentiality. 2. Application procedure Applicants requesting access to data from the TKI-BTRP_DAC will be asked to complete a basic application form and to agree to the terms and conditions laid out in the Data Access Agreement (DAA). The DAA must be signed by both the applicant and the relevant Head of Department, Head of Institute, or equivalent. Where the applicant is the Head of Department, a countersignature from another officer authorized to sign material transfer agreements on behalf of the institution must be provided. Successful applicants who have access to data will be designated "Registered Users" and will be issued with a username and password by the EGA to enable access to the database. The Committee will consider applications that include named collaborators, but each Institution must sign a separate Data Access Agreement. Should you wish to share the data with additional collaborators not previously approved, they must make a separate application for access to the Data. Applicants agree to use the data for the approved purpose and project described in the application; use of the data for a new purpose or project will require a new application and approval. Details of the application procedure, along with the relevant forms, can be found at under the 'Access to Data' tab. 3. Membership of TKI_BTRP Data Access Committee Dr Raelene Endersby, (Chair), Joint Head, Brain Tumour Research, Telethon Kids Institute Dr Nick Gottardo, Joint Head, Brain Tumour Research, Telethon Kids Institute Dr Jacqueline Whitehouse, Senior Research Officer, Brain Tumour Research, Telethon Kids Institute Ms Emma Stone, Program Manager, Telethon Kids Cancer Centre, Telethon Kids Institute 4. Assessment Criteria Each application will be assessed to determine if: • it has been submitted by a qualified researcher or researchers, embedded in a recognised institution that can provide institutional responsibility for appropriate research governance • the project described constitutes 'biomedical health‐related research' in the context of the consent process, and is likely to be understood as such by the sample donors • it breaches any of the ethical permissions or restrictions in the consent forms for any component cohort or collection • it has the potential to produce information that will enable identification of individual participants • that PhD students include details of their research supervisors In considering applications, the TKI-BTRP_DAC have clarified their policies in regard to specific data access requests. The Committee has agreed that: • TKI-BTRP_DAC does NOT attempt to peer review the scientific quality of proposals. However, it does ask for a brief summary of the research to be undertaken, in order to judge whether it falls within the scope of the consents. It also considers that grossly inadequate research is ethically questionable, and reserves the right to refer back for clarification those requests that do not appear to attain even a minimal standard of competence • the use of data by commercial companies for commercial purposes is NOT permitted 5. Availability of samples DNA, RNA or tissue samples are not available through the Data Access Committee.

DATA ACCESS TERMS AND CONDITIONS FOR TELETHON KIDS INSTITUTE BRAIN TUMOUR RESEARCH MOLECULAR GENETICS STUDIES Party providing access to Data: TELETHON KIDS INSTITUTE (ABN 86 009 278 755) of Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, Western Australia 6009 (Telethon Kids) Recipient: INSERT NAME (insert ABN if applicable) of insert address The terms and conditions set out below govern the terms on which access will be granted to Beadchip-data, transcriptome, methylome or sequence-derived DNA variant data generated by the Brain Tumour Research team based in the Telethon Kids Cancer Centre at the Telethon Kids Institute, Perth, Western Australia, including studies carried out in collaboration with the Children’s Cancer Institute, Sydney, New South Wales, and other international collaborators. In signing this document, You are agreeing to be bound by the terms and conditions of access set out below. For the sake of clarity, the terms of access set out below apply both to the User and the User’s Institution (as defined below). Definitions: Agreement means this document which outlines the terms and conditions on which the Recipient is to access and use the Data. Authorised Personnel means the individuals at the User Institution to whom Telethon Kids 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. BTRP means the Brain Tumour Research Program based at the Telethon Kids Institute. Commercial Purpose means the sale, lease, license, or other transfer of the Data to a for-profit organisation. Commercial Purposes shall also include uses of the Data by any organisation, including the Recipient, to perform contract research, to screen compound libraries, to produce or manufacture products for general sale, or to conduct research activities that result in any sale, lease, license, or transfer of the Data to a for-profit organisation. However, industrially sponsored academic research shall not be considered a use of the Data for Commercial Purposes per se, unless any of the above conditions of this definition are met. Confidential Information means any and all technical, scientific, educational, process, data, documents, materials, copyright, concept, invention, patent or patent application, trademark or trademark application, trade secrets, know-how, or other information of the User which is: (a) provided by Telethon Kids and the User/User Institution for the purposes of this Agreement or the Project and marked “confidential” or notified as confidential, in writing, at the time of it being provided; or (b) created by the User or otherwise coming into existence pursuant to this Agreement or as a result of the Project and is claimed in writing at such time to be confidential. Information is not confidential if: (a) it is or becomes part of the public domain unless it came into the public domain by a breach of confidentiality; (b) it is obtained lawfully from a third party without any breach of confidentiality; (c) it is already known by the BTRP (as shown by written record) before the date of disclosure to it; (d) it is independently developed by an employee of the User Institution who has no knowledge of the disclosure under this Agreement; or (e) it is required to be disclosed by a court, rule or governmental law or regulation, or the rules of any stock exchange, provided that the User making the disclosure provides prompt notice to Telethon Kids of any such requirement. Data means all and any human genetic data obtained from the BTRP. Data Producers means the BTRP and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. Data Subject means a person, who has been informed of the purpose for which the Data is held and has given his/her informed consent thereto. EGA means the European Genome-phenome Archive, which distributes BTRP molecular data. External Collaborator means a collaborator of the User, working for an institution other than the User Institution. Project means 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 means, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. User means a researcher whose User Institution has previously completed this Agreement and has received acknowledgement of its acceptance. User Institution means the organisation at which the User is employed, affiliated or enrolled. TKI-BTRP Data Access Committee means the committee who reviews applications to access data and approves access. You and Your means the User Institution and User jointly. Terms and Conditions: In signing this Agreement: 1. You agree to use the Data only for the advancement of medical research, according to the consent obtained from sample donors. 2. You agree not to use the Data or any part thereof for the creation of products for sale or for any Commercial Purpose. 3. You agree to preserve, at all times, the confidentiality of information and Data pertaining to Data Subjects. In particular, You undertake not to use, or attempt to use the Data to compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy. 4. You agree not to attempt to link the data provided under this Agreement to other information or archive data available for the data sets provided, even if access to that data has been formally granted to you, or it is freely available without restriction, without specific permission being sought from the TKI-BTRP Data Access Committee. 5. You agree only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel (details of which are set out in APPENDIX II), except as necessary for data/safety monitoring or programme management. Should You wish to share the Data with a collaborator outside of Your Institution, the third party must make a separate application for access to the Data. 6. You agree to use the Data for the approved purpose and project described in your application (details of which are set out in APPENDIX I); use of the data for a new purpose or project will require a new application and approval. 7. In the exceptional circumstance that we establish a Data access account using a non-institutional email address, You will inform the EGA if you move or change User Institution. 8. You accept that Data will be reissued from time to time, with suitable versioning. If the reissue is at the request of sample donors and/or other ethical scrutiny, You will destroy earlier versions of the Data. 9. You agree to follow the Fort Lauderdale Guidelines ( ) and the Toronto Statement ( This includes but is not limited to recognising the contribution of the Data Producers (BTRP) and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 10. You agree to abide by the terms outlined in the 'Publications Policy' as set out 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. 11. You accept that the BTRP, the original data creators, depositors or copyright holders, or the funders of the Data or any part of the Data supplied: a) bear no legal responsibility for the accuracy or comprehensiveness of the Data; and b) accept no liability for indirect, consequential, or incidental, damages or losses arising from use of the Data, or from the unavailability of, or break in access to, the Data for whatever reason. 12. You understand and acknowledge that the Data is protected by copyright and other intellectual property rights which are the property of Telethon Kids, and that duplication, except as reasonably required to carry out Your research with the Data, or sale of all or part of the Data on any media is not permitted. 13. You recognise that nothing in this Agreement shall operate to transfer to the User Institution any intellectual property rights relating to the Data. The User Institution has the right to develop intellectual property based on comparisons with their own data. 14. (a) This Agreement shall commence on the last date this Agreement is signed by You and the User Institution, and will continue in force unless terminated in accordance with this clause. (b) Telethon Kids and/or You may terminate this Agreement at any time by providing thirty (30) days written notice to the other. (c) Upon expiration of this Agreement or termination by written notice, whichever is earliest, You shall, within fourteen (14) days of Telethon Kids’ request, destroy (or permanently delete) all Data in Your possession or control. (d) You accept that this Agreement will terminate immediately upon any breach of this Agreement by You and You will be required to destroy any Data held. 15. You accept that it may be necessary for the BTRP, or their appointed agents to alter the terms of this Agreement from time to time in order to address new concerns. In this event, You will be contacted and informed of any changes and Your continued use of the Data shall be dependent on all parties entering into a new version of the Agreement. 16. You agree that You will submit a report to the TKI-BTRP Data Access Committee, if requested, on completion of the agreed purpose. The TKI-BTRP Data Access Committee agrees to treat the report and all information, data, results, and conclusions contained within such report as Confidential Information belonging to the User Institution. 17. You accept that the Data is protected by and subject to national laws, including but not limited to the Privacy Act 1988 (Cth), and that You are responsible for ensuring compliance with any such applicable laws. The TKI-BTRP Data Access Committee reserves the right to request and inspect data security and management documentation to ensure the adequacy of data protection measures in countries that have no national laws comparable to that which pertain in Australia. 18. Without prejudice to any right of a party to institute proceedings in a court of competent jurisdiction, any dispute between the parties shall, in good faith, first be sought to be resolved by negotiation between each party’s nominated representative. If the dispute is not resolved within 20 days, the parties will explore alternative dispute resolution methods. 19. This Agreement shall be governed by the laws of Western Australia and the Parties agree to submit to the non-exclusive jurisdiction of the Courts of that jurisdiction.   Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: WHEN SUBMITTING THIS DOCUMENT PLEASE INCLUDE ALL PAGES OF THE AGREEMENT WITH THIS SIGNATURE PAGE   APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I DATASET DETAILS Small molecule screen reveals synergy of cell cycle checkpoint kinase inhibitors with DNA-damaging chemotherapies in medulloblastoma EGAS00001004748 Name of project that created the dataset Small molecule screen reveals synergy of cell cycle checkpoint kinase inhibitors with DNA-damaging chemotherapies in medulloblastoma Names of other data producers/collaborators Raelene Endersby1,2*, Jacqueline Whitehouse1,2, Marcel Kool3,4, Nicholas G Gottardo1,2,5‡* Affiliations 1. Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia, 6009. 2. Division of Paediatrics/Centre for Child Health Research, Medical School, University of Western Australia, Crawley, WA, Australia, 6009. 3. Hopp Children’s Cancer Center (KiTZ) and German Cancer Research Center (DKFZ) 4. Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands, 3584 CS. 5. Department of Pediatric and Adolescent Oncology/Hematology, Perth Children's Hospital, Nedlands, WA, Australia, 6009.   Specific limitations on areas of research Data Use Conditions: Term Label Description Primary Terms DUO:0000006 health/medical/biomedical research and clinical care This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. Secondary Terms (can be one or more extra conditions, in addition to one primary term) DUO:0000014 research use only This secondary category consent code indicates that use is limited to research purposes (e.g., does not include its use in clinical care). DUO:0000019 publication required This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. DUO:0000024 publication moratorium This requirement indicates that requestor agrees not to publish results of studies until a specific date. DUO:0000025 time limit on use This requirement indicates that use is approved for a specific number of months. DUO:0000026 user-specific restriction This requirement indicates that use is limited to use by approved users. 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 Publications Policy The release of pre-publication data from large resource-generating scientific projects was the subject of a meeting held in January 2003, the “Fort Lauderdale meeting”, sponsored by the Wellcome Trust. The report from that meeting can be viewed at The recommendations of the Fort Lauderdale meeting address the roles and responsibilities of data producers, data users, and funders of ‘community resource projects’, with the aim of establishing and maintaining an appropriate balance between the interests of data users in rapid access to data and the needs of data producers to receive recognition for their work. The Telethon Kids Institute has agreed to follow these data-release principles and as such, these data are being released as a ‘community resource project’ as defined in the report of the Fort Lauderdale meeting. The Telethon Kids Institute, as data producers, reserve the right to publish the initial global analyses of the data. In so doing, it will also ensure that the data generated are fully described. Brain Tumour Research Program (BTRP) 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. BTRP 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 6 months after these data were first made available on the relevant hosting database, unless BTRP 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 number (EGAS00001004709), and acknowledge its use in a form agreed by the User Institution with BTRP. Acknowledgement Authors who use data from the Telethon Kids Institute Brain Tumour Research projects must acknowledge the source using the following wording “This study makes use of data generated by the Telethon Kids Institute and we acknowledge the generous donation of tissue samples by patients and their families.” You are also requested to cite the relevant primary publication: Raelene Endersby, Jacqueline Whitehouse, Allison Pribnow, Mani Kuchibhotla, Hilary Hii, Brooke Carline, Suresh Gande, Jennifer Stripay, Mathew Ancliffe, Meegan Howlett, Tobias Schoep, Courtney George, Clara Andradas, Patrick Dyer, Marjolein Schluck, Brett Patterson, Silvia K Tacheva-Gigorova, Matthew N Cooper, Giles Robinson, Clinton Stewart, Stefan M Pfister, Marcel Kool, Till Milde, Amar Gajjar, Terrance Johns, Robert J Wechsler-Reya, Martine F Roussel, Nicholas G Gottardo. Small molecule screen reveals synergy of cell cycle checkpoint kinase inhibitors with DNA-damaging chemotherapies in medulloblastoma. Under Review. Users should note that the Telethon Kids Institute and/or Individual Investigators bear no responsibility for the further analysis or interpretation of these data, over and above that published by the Institute.

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
EGAS00001004748 RNASeq
ID File Type Size Located in
EGAF00004724159 fastq.gz 770.6 MB
EGAF00004724160 fastq.gz 765.5 MB
EGAF00004724161 fastq.gz 900.2 MB
EGAF00004724162 fastq.gz 897.7 MB
EGAF00004724163 fastq.gz 10.6 GB
EGAF00004724164 fastq.gz 10.1 GB
EGAF00004725256 fastq.gz 8.8 GB
EGAF00004725257 fastq.gz 8.3 GB
8 Files (41.2 GB)