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RNA-Seq and small RNA-Seq of tuberous sclerosis complex cortical tubers and age-matched controls.

This dataset contains both standard RNA-Seq and small RNA-Seq of TSC related cortical tubers and age matched cortical controls. For the standard RNA-Seq paired-end sequencing was carried out. Each sample was split across multiple lanes. For the files available here the multiple lanes have been merged together, resulting in one forward and one reverse .fastq file for each sample. Small RNA-Seq was carried out on the same samples that underwent standard RNA-Seq. Again paired-end sequencing was carried out. The files here are raw and will need to be undergo quality control and trimming.

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Data Access Agreement: Coding and small non-coding transcriptional landscape of tuberous sclerosis complex cortical tubers: implications for pathophysiology and treatment

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 Authorised Personnel: The individuals at the User Institution to whom James D. Mills and Eleonora Aronica 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. Data: The managed access datasets to which the User Institution has requested access. Data Producers: James D. Mills, Eleonora Aronica and the collaborators listed in Appendix I responsible for the development, organisation, 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. 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 Authorised 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/docu ments/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 recognising 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 analysing 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.p df ) 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 James D. Mills and Eleonora Aronica within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify James D. Mills and Eleonora Aronica prior to any significant changes to the protocol for the Project. 14. The User Institution will notify James D. Mills and Eleonora Aronica as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. James D. Mills and Eleonora Aronica 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 James D. Mills and Eleonora Aronica. 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 Authorised Personnel. The User Institution will procure that the Authorised 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 Netherlands and shall be subject to the exclusive jurisdiction of the Netherlands 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: Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II – PROJECT DETAILS APPENDIX III – PUBLICATION POLICY APPENDIX 1 - DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) EGAS00001002485: small RNA-Seq and RNA-Seq of cortical tubers from sufferers of tuberous sclerosis complex and matched controls. Name of project that created the dataset Coding and small non-coding transcriptional landscape of tuberous sclerosis complex cortical tubers: implications for pathophysiology and treatment Names of other data producers/collaborators Anand M. Iyer, Jackelien van Scheppingen, Anika Bongaarts, Jasper J. Anink, Bart Janssen, Till S. Zimmer, Wim G. Spliet, Peter C. van Rijen, Floor E. Jansen, Martha Feycht, Johannes A. Hainfellner, Pavel Krsek, Josef Zamecnik, Katarzyna Kotulska, Sergiusz Jozwiak, Anna Jansen, Lieven Lagae, Paolo Curatolo, David J. Kwiatkowski, R. Jeroen Pasterkamp, Ketharini Senthikumar, Lars von Oerthel, Marco F. Hoekman, Jan A. Gorter, Peter B. Crino, Angelika Mühlebener, Brandon P. Scicluna Specific limitations on areas of research This data is to be used for academic research only. Data availability This dataset will be available for download from the 1st of August 2018. 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.

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
EGAS00001002485 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
EGAF00001698121 fastq.gz 1.5 GB
EGAF00001698122 fastq.gz 1.6 GB
EGAF00001698123 fastq.gz 2.3 GB
EGAF00001698124 fastq.gz 2.3 GB
EGAF00001698125 fastq.gz 1.7 GB
EGAF00001698126 fastq.gz 1.8 GB
EGAF00001698127 fastq.gz 1.6 GB
EGAF00001698128 fastq.gz 1.6 GB
EGAF00001698129 fastq.gz 1.6 GB
EGAF00001698130 fastq.gz 1.6 GB
EGAF00001698131 fastq.gz 1.7 GB
EGAF00001698132 fastq.gz 1.8 GB
EGAF00001698133 fastq.gz 1.6 GB
EGAF00001698134 fastq.gz 1.6 GB
EGAF00001698135 fastq.gz 1.5 GB
EGAF00001698136 fastq.gz 1.6 GB
EGAF00001698137 fastq.gz 2.2 GB
EGAF00001698138 fastq.gz 2.2 GB
EGAF00001698139 fastq.gz 1.8 GB
EGAF00001698140 fastq.gz 1.8 GB
EGAF00001698141 fastq.gz 1.6 GB
EGAF00001698142 fastq.gz 1.7 GB
EGAF00001698143 fastq.gz 1.8 GB
EGAF00001698144 fastq.gz 1.9 GB
EGAF00001698145 fastq.gz 1.8 GB
EGAF00001698146 fastq.gz 1.8 GB
EGAF00001698147 fastq.gz 1.8 GB
EGAF00001698148 fastq.gz 1.8 GB
EGAF00001698149 fastq.gz 2.5 GB
EGAF00001698150 fastq.gz 2.6 GB
EGAF00001698151 fastq.gz 1.5 GB
EGAF00001698152 fastq.gz 1.6 GB
EGAF00001698153 fastq.gz 1.7 GB
EGAF00001698154 fastq.gz 1.8 GB
EGAF00001698155 fastq.gz 2.1 GB
EGAF00001698156 fastq.gz 2.2 GB
EGAF00001698157 fastq.gz 2.9 GB
EGAF00001698158 fastq.gz 2.9 GB
EGAF00001698159 fastq.gz 3.1 GB
EGAF00001698160 fastq.gz 3.2 GB
EGAF00001698161 fastq.gz 2.8 GB
EGAF00001698162 fastq.gz 2.9 GB
EGAF00001698163 fastq.gz 2.7 GB
EGAF00001698164 fastq.gz 2.8 GB
EGAF00001698165 fastq.gz 689.7 MB
EGAF00001698166 fastq.gz 770.5 MB
EGAF00001698167 fastq.gz 475.1 MB
EGAF00001698168 fastq.gz 480.8 MB
EGAF00001698169 fastq.gz 504.2 MB
EGAF00001698170 fastq.gz 525.9 MB
EGAF00001698171 fastq.gz 650.8 MB
EGAF00001698172 fastq.gz 677.2 MB
EGAF00001698173 fastq.gz 154.6 MB
EGAF00001698174 fastq.gz 141.0 MB
EGAF00001698175 fastq.gz 171.7 MB
EGAF00001698176 fastq.gz 201.5 MB
EGAF00001698177 fastq.gz 145.5 MB
EGAF00001698178 fastq.gz 164.8 MB
EGAF00001698179 fastq.gz 162.5 MB
EGAF00001698180 fastq.gz 187.9 MB
EGAF00001698181 fastq.gz 129.4 MB
EGAF00001698182 fastq.gz 154.8 MB
EGAF00001698183 fastq.gz 166.9 MB
EGAF00001698184 fastq.gz 187.3 MB
EGAF00001698185 fastq.gz 376.5 MB
EGAF00001698186 fastq.gz 393.5 MB
EGAF00001698187 fastq.gz 709.5 MB
EGAF00001698188 fastq.gz 725.4 MB
EGAF00001698189 fastq.gz 574.3 MB
EGAF00001698190 fastq.gz 646.0 MB
EGAF00001698191 fastq.gz 568.0 MB
EGAF00001698192 fastq.gz 594.5 MB
EGAF00001698193 fastq.gz 652.4 MB
EGAF00001698194 fastq.gz 692.9 MB
EGAF00001698195 fastq.gz 541.9 MB
EGAF00001698196 fastq.gz 546.4 MB
EGAF00001698197 fastq.gz 678.5 MB
EGAF00001698198 fastq.gz 693.6 MB
EGAF00001698199 fastq.gz 696.9 MB
EGAF00001698200 fastq.gz 748.4 MB
EGAF00001698201 fastq.gz 703.2 MB
EGAF00001698202 fastq.gz 751.5 MB
EGAF00001698203 fastq.gz 473.7 MB
EGAF00001698204 fastq.gz 516.6 MB
EGAF00001698205 fastq.gz 571.8 MB
EGAF00001698206 fastq.gz 592.8 MB
EGAF00001698207 fastq.gz 274.9 MB
EGAF00001698208 fastq.gz 278.4 MB
88 Files (109.7 GB)