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Targeting Heterochromatin Eliminates Malignant Stem Cells in Chronic Myelomonocytic Leukemia Through Reactivation of Retroelements and Innate Immune pathways

RNA-sequencing, ATAC-sequencing, CUT&Tag-sequencing, data from CMML patient and aged-matched healthy donor CD34+ cells. RNA-sequencing data from patient CD34+ cells after treatment for 4 days with decitabine or UNC0638 inhibitors, alone or together, or left untreated

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DATA ACCESS AGREEMENT Gustave Roussy

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 Authorized Personnel: The individuals at the User Institution to whom the Data Access Committee 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 Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The individuals, listed in Appendix I, responsible for the development, organization, 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(s) that has requested access to the Data (detailed in Appendix II). Data Producers Institution(s): The Institution(s) that has produced the Data (detailed in Appendix I). Data Access Committee: The committee responsible for authorizing access to the data. Committee members are listed in Appendix I. 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 Authorized 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 (https://www.sanger.ac.uk/wp-content/uploads/fortlauderdalereport.pdf) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognizing the contribution of the Data Producers and including a proper acknowledgment 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 analyzing 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.ott.nih.gov/sites/default/files/documents/pdfs/70fr18413.pdf) in conformity with the Organization for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (https://www.oecd.org/sti/emerging-tech/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 the Data Access Committee within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify the Data Access Committee prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the Data Access Committee as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The Data Access Committee 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. 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 Authorized Personnel. The User Institution will procure that the Authorized 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 France and shall be subject to the exclusive jurisdiction of the France courts. Agreed for User Institution (Name, Title, Date, Signature): Principal Investigator (Name, Title, Date, Signature): I confirm that I have read and understood this Agreement. Agreed for the Data Access Committee (Name, Title, Date, Signature): APPENDIX I – DATASET DETAILS & DATA ACCESS COMMITTEE APPENDIX II – PROJECT DETAILS APPENDIX III – PUBLICATION POLICY APPENDIX I – DATASET DETAILS & DATA ACCESS COMMITTEE Dataset reference (EGA Study ID, Dataset Accession Numbers and Dataset Details): Name of the project that created the dataset : Targeting Heterochromatin Eliminates Malignant Stem Cells in Chronic Myelomonocytic Leukemia Through Reactivation of Retroelements and Innate Immune pathways Data Producers Institution(s): Gustave Roussy, 114, rue Edouard Vaillant – 94805 VILLEJUIF Cedex, FRANCE Names of other data producers/collaborators (Name, Email, Job Title): Specific limitations on areas of research: 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. Name of the Data Access Committee: DAC Dr. F. PORTEU – Gustave Roussy Data Access Committee Members (Name, Email, Job Title): Principal Investigator Françoise PORTEU (FRANCOISE.PORTEU@gustaveroussy.fr) Head of Bioinformatics platform DELOGER Marc (Marc.DELOGER@gustaveroussy.fr) Data Protection Officer BECHET Clara (Clara.BECHET@gustaveroussy.fr) 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): User Institution(s): All Individuals who the User Institution to be named as registered users (Name, Email, Job Title, Supervisor): All Individuals that should have an account created at the EGA (Name, Email, Job Title): APPENDIX III – PUBLICATION POLICY The Data Access Committee anticipates 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 the Data Access Committee have published their own global analysis or twelve (12) months after these data were first made available on the relevant hosting database, unless the Data Access Committee 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 numbers (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with the Data Access Committee.

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
EGAS50000000367 Epigenetics

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
EGAF50000121150 fastq.gz 746.6 MB
EGAF50000121151 fastq.gz 741.7 MB
EGAF50000121152 fastq.gz 3.1 GB
EGAF50000121153 fastq.gz 3.3 GB
EGAF50000121154 fastq.gz 4.4 GB
EGAF50000121155 fastq.gz 4.7 GB
EGAF50000121156 fastq.gz 309.8 MB
EGAF50000121157 fastq.gz 352.2 MB
EGAF50000121158 fastq.gz 563.1 MB
EGAF50000121159 fastq.gz 580.2 MB
EGAF50000121160 fastq.gz 567.2 MB
EGAF50000121161 fastq.gz 530.0 MB
EGAF50000121162 fastq.gz 571.4 MB
EGAF50000121163 fastq.gz 493.6 MB
EGAF50000121164 fastq.gz 918.1 MB
EGAF50000121165 fastq.gz 950.0 MB
EGAF50000121166 fastq.gz 672.4 MB
EGAF50000121167 fastq.gz 704.9 MB
EGAF50000121168 fastq.gz 8.9 GB
EGAF50000121169 fastq.gz 9.5 GB
EGAF50000121170 fastq.gz 9.1 GB
EGAF50000121171 fastq.gz 8.4 GB
EGAF50000121172 fastq.gz 5.7 GB
EGAF50000121173 fastq.gz 5.5 GB
EGAF50000121174 fastq.gz 5.9 GB
EGAF50000121175 fastq.gz 6.2 GB
EGAF50000121176 fastq.gz 6.0 GB
EGAF50000121177 fastq.gz 6.2 GB
EGAF50000121178 fastq.gz 8.6 GB
EGAF50000121179 fastq.gz 9.1 GB
EGAF50000121180 fastq.gz 6.0 GB
EGAF50000121181 fastq.gz 6.3 GB
EGAF50000121182 fastq.gz 7.1 GB
EGAF50000121183 fastq.gz 7.4 GB
EGAF50000121184 fastq.gz 5.6 GB
EGAF50000121185 fastq.gz 6.0 GB
EGAF50000121186 fastq.gz 4.5 GB
EGAF50000121187 fastq.gz 4.7 GB
EGAF50000121188 fastq.gz 3.0 GB
EGAF50000121189 fastq.gz 2.7 GB
EGAF50000121190 fastq.gz 2.1 GB
EGAF50000121191 fastq.gz 2.4 GB
EGAF50000121192 fastq.gz 2.6 GB
EGAF50000121193 fastq.gz 2.9 GB
EGAF50000121194 fastq.gz 3.0 GB
EGAF50000121195 fastq.gz 2.7 GB
EGAF50000121196 fastq.gz 2.2 GB
EGAF50000121197 fastq.gz 2.4 GB
EGAF50000121198 fastq.gz 4.5 GB
EGAF50000121199 fastq.gz 4.9 GB
EGAF50000121200 fastq.gz 1.9 GB
EGAF50000121201 fastq.gz 1.8 GB
EGAF50000121202 fastq.gz 2.2 GB
EGAF50000121203 fastq.gz 2.4 GB
EGAF50000121204 fastq.gz 1.4 GB
EGAF50000121205 fastq.gz 1.5 GB
EGAF50000121206 fastq.gz 4.0 GB
EGAF50000121207 fastq.gz 4.3 GB
EGAF50000121208 fastq.gz 1.4 GB
EGAF50000121209 fastq.gz 1.6 GB
EGAF50000121210 fastq.gz 1.4 GB
EGAF50000121211 fastq.gz 1.6 GB
EGAF50000121212 fastq.gz 1.5 GB
EGAF50000121213 fastq.gz 1.3 GB
EGAF50000121214 fastq.gz 1.9 GB
EGAF50000121215 fastq.gz 2.1 GB
EGAF50000121216 fastq.gz 1.5 GB
EGAF50000121217 fastq.gz 1.7 GB
EGAF50000121218 fastq.gz 2.8 GB
EGAF50000121219 fastq.gz 3.2 GB
EGAF50000121220 fastq.gz 1.8 GB
EGAF50000121221 fastq.gz 2.0 GB
EGAF50000121222 fastq.gz 1.6 GB
EGAF50000121223 fastq.gz 1.8 GB
EGAF50000121224 fastq.gz 1.6 GB
EGAF50000121225 fastq.gz 1.7 GB
EGAF50000121226 fastq.gz 2.2 GB
EGAF50000121227 fastq.gz 2.5 GB
EGAF50000121228 fastq.gz 1.4 GB
EGAF50000121229 fastq.gz 1.6 GB
EGAF50000121230 fastq.gz 1.1 GB
EGAF50000121231 fastq.gz 1.2 GB
EGAF50000121232 fastq.gz 1.8 GB
EGAF50000121233 fastq.gz 2.0 GB
EGAF50000121234 fastq.gz 1.6 GB
EGAF50000121235 fastq.gz 1.8 GB
EGAF50000121236 fastq.gz 1.9 GB
EGAF50000121237 fastq.gz 2.1 GB
EGAF50000121238 fastq.gz 966.0 MB
EGAF50000121239 fastq.gz 1.1 GB
EGAF50000121240 fastq.gz 1.4 GB
EGAF50000121241 fastq.gz 1.2 GB
EGAF50000121242 fastq.gz 1.2 GB
EGAF50000121243 fastq.gz 1.4 GB
EGAF50000121244 fastq.gz 1.5 GB
EGAF50000121245 fastq.gz 1.7 GB
EGAF50000121246 fastq.gz 1.3 GB
EGAF50000121247 fastq.gz 1.4 GB
EGAF50000121248 fastq.gz 1.5 GB
EGAF50000121249 fastq.gz 1.7 GB
EGAF50000121250 fastq.gz 1.7 GB
EGAF50000121251 fastq.gz 1.9 GB
EGAF50000121252 fastq.gz 1.1 GB
EGAF50000121253 fastq.gz 1.3 GB
EGAF50000121254 fastq.gz 2.5 GB
EGAF50000121255 fastq.gz 2.4 GB
EGAF50000121256 fastq.gz 1.9 GB
EGAF50000121257 fastq.gz 1.9 GB
EGAF50000121258 fastq.gz 2.5 GB
EGAF50000121259 fastq.gz 2.4 GB
EGAF50000121260 fastq.gz 3.4 GB
EGAF50000121261 fastq.gz 3.4 GB
EGAF50000121262 fastq.gz 1.8 GB
EGAF50000121263 fastq.gz 1.7 GB
EGAF50000121264 fastq.gz 2.4 GB
EGAF50000121265 fastq.gz 2.5 GB
EGAF50000121266 fastq.gz 3.7 GB
EGAF50000121267 fastq.gz 3.3 GB
EGAF50000121268 fastq.gz 5.0 GB
EGAF50000121269 fastq.gz 4.7 GB
EGAF50000121270 fastq.gz 13.8 GB
EGAF50000121271 fastq.gz 14.3 GB
EGAF50000121272 fastq.gz 5.2 GB
EGAF50000121273 fastq.gz 5.4 GB
EGAF50000121274 fastq.gz 8.4 GB
EGAF50000121275 fastq.gz 8.8 GB
EGAF50000121276 fastq.gz 4.3 GB
EGAF50000121277 fastq.gz 4.1 GB
EGAF50000121278 fastq.gz 6.5 GB
EGAF50000121279 fastq.gz 6.2 GB
EGAF50000121280 fastq.gz 6.1 GB
EGAF50000121281 fastq.gz 6.4 GB
EGAF50000121282 fastq.gz 6.3 GB
EGAF50000121283 fastq.gz 6.0 GB
EGAF50000121284 fastq.gz 1.1 GB
EGAF50000121285 fastq.gz 1.2 GB
EGAF50000121286 fastq.gz 2.2 GB
EGAF50000121287 fastq.gz 2.5 GB
EGAF50000121288 fastq.gz 2.4 GB
EGAF50000121289 fastq.gz 2.2 GB
EGAF50000121290 fastq.gz 1.4 GB
EGAF50000121291 fastq.gz 1.6 GB
EGAF50000121292 fastq.gz 964.5 MB
EGAF50000121293 fastq.gz 1.1 GB
EGAF50000121294 fastq.gz 1.3 GB
EGAF50000121295 fastq.gz 1.4 GB
EGAF50000121296 fastq.gz 1.4 GB
EGAF50000121297 fastq.gz 1.6 GB
148 Files (460.9 GB)