Need Help?

Orthotopic murine Group 3 medulloblastoma in C57Bl/6 mice treated with saline, cyclophosphamide or gemcitabine

Mice with medulloblastoma (Group 3) were treated with saline, cyclophosphamide, or gemcitabine as described by Abbas et al (2020). Total RNA was isolated with RNeasy Plus Mini Kit (Qiagen), library preparation (SureSelect, Agilent), rRNA depletion (Ribo-Zero Plus, Illumina) and sequencing were carried out by GenomicsWA or Australian Genome Research Facility. Libraries were sequenced on NovaSeq 6000 S1 flow cells as paired-end 150bp reads (Illumina).

Request Access

DATA ACCESS AGREEMENT – BRAIN TUMOUR RESEARCH, TELETHON KIDS CANCER CENTRE. 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.

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. 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. 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 (EGAS00001005847 or EGAS00001005846), 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.” You are also requested to cite the relevant primary publication: Zahra Abbas, Courtney George, Mathew Ancliffe, Meegan Howlett, Anya C Jones, Mani Kuchibhotla, Robert J. Wechsler-Reya, Nicholas G Gottardo, Raelene Endersby*. Conventional Therapies Deplete Brain-Infiltrating Adaptive Immune Cells in a Mouse Model of Group 3 Medulloblastoma Implicating Myeloid Cells as Favorable Immunotherapy Targets. Frontiers in Immunology, 2022 (under revision). 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
EGAS00001005846 RNASeq
ID File Type Size Located in
EGAF00005787706 fastq.gz 4.4 GB
EGAF00005787707 fastq.gz 5.0 GB
EGAF00005787708 fastq.gz 3.5 GB
EGAF00005787709 fastq.gz 4.0 GB
EGAF00005787710 fastq.gz 2.4 GB
EGAF00005787711 fastq.gz 2.6 GB
EGAF00005787712 fastq.gz 4.2 GB
EGAF00005787713 fastq.gz 4.6 GB
EGAF00005787714 fastq.gz 3.3 GB
EGAF00005787715 fastq.gz 3.7 GB
EGAF00005787716 fastq.gz 2.9 GB
EGAF00005787717 fastq.gz 3.2 GB
EGAF00005787718 fastq.gz 3.1 GB
EGAF00005787719 fastq.gz 3.5 GB
EGAF00005787720 fastq.gz 2.9 GB
EGAF00005787721 fastq.gz 3.2 GB
EGAF00005787722 fastq.gz 3.1 GB
EGAF00005787723 fastq.gz 3.5 GB
EGAF00005787724 fastq.gz 4.0 GB
EGAF00005787725 fastq.gz 4.5 GB
EGAF00005787726 fastq.gz 3.8 GB
EGAF00005787727 fastq.gz 4.3 GB
EGAF00005787728 fastq.gz 3.1 GB
EGAF00005787729 fastq.gz 3.5 GB
EGAF00005787730 fastq.gz 4.0 GB
EGAF00005787731 fastq.gz 4.4 GB
EGAF00005787732 fastq.gz 4.3 GB
EGAF00005787733 fastq.gz 4.8 GB
EGAF00005787734 fastq.gz 3.4 GB
EGAF00005787735 fastq.gz 3.8 GB
EGAF00005787736 fastq.gz 2.6 GB
EGAF00005787737 fastq.gz 3.0 GB
EGAF00005787738 fastq.gz 3.5 GB
EGAF00005787739 fastq.gz 4.0 GB
EGAF00005787740 fastq.gz 3.5 GB
EGAF00005787741 fastq.gz 3.9 GB
EGAF00005787742 fastq.gz 3.1 GB
EGAF00005787743 fastq.gz 3.5 GB
EGAF00005787744 fastq.gz 3.3 GB
EGAF00005787745 fastq.gz 3.7 GB
40 Files (144.8 GB)