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Finding structural variation and functional consequences from the primary leukemia cells (CLL) at the single-cell level

In this study, we aimed to identify somatic structural variation of chronic lymphocytic leukemia (CLL) at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from 63-year-old female patient.

Request Access

This is the data access policy for the Single cell multi-omics (scNOVA) group for CLL)

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 Single cell multi-omics (scNOVA) group for CLL 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: Single cell multi-omics (scNOVA) group for CLL 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. 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/documents/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.pdf ) 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 Single cell multi-omics (scNOVA) group for CLL within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Single cell multi-omics (scNOVA) group for CLL prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Single cell multi-omics (scNOVA) group for CLL as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Single cell multi-omics (scNOVA) group for CLL 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 Single cell multi-omics (scNOVA) group for CLL. 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 England and Wales and shall be subject to the exclusive jurisdiction of the English 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 XXXXX Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) Name of project that created the dataset Names of other data producers/collaborators Specific limitations on areas of research 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 – PUBLICATION POLICY Single cell multi-omics (scNOVA) group for CLL 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. Single cell multi-omics (scNOVA) group for CLL 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 XX months after these data were first made available on the relevant hosting database, unless Single cell multi-omics (scNOVA) group for CLL 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 Single cell multi-omics (scNOVA) group for CLL.

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
EGAS00001004925 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
EGAF00004956044 txt.gz 98.6 MB
EGAF00004956045 txt.gz 99.6 MB
EGAF00004956046 txt.gz 52.8 MB
EGAF00004956047 txt.gz 53.3 MB
EGAF00004956048 txt.gz 153.7 MB
EGAF00004956049 txt.gz 155.4 MB
EGAF00004956050 txt.gz 159.6 MB
EGAF00004956051 txt.gz 161.2 MB
EGAF00004956052 txt.gz 140.5 MB
EGAF00004956053 txt.gz 142.0 MB
EGAF00004956054 txt.gz 179.4 MB
EGAF00004956055 txt.gz 180.5 MB
EGAF00004956056 txt.gz 58.0 MB
EGAF00004956057 txt.gz 58.8 MB
EGAF00004956058 txt.gz 45.7 MB
EGAF00004956059 txt.gz 46.2 MB
EGAF00004956060 txt.gz 84.3 MB
EGAF00004956061 txt.gz 85.1 MB
EGAF00004956062 txt.gz 133.1 MB
EGAF00004956063 txt.gz 134.8 MB
EGAF00004956064 txt.gz 326.6 MB
EGAF00004956065 txt.gz 330.0 MB
EGAF00004956066 txt.gz 58.5 MB
EGAF00004956067 txt.gz 59.3 MB
EGAF00004956068 txt.gz 244.2 MB
EGAF00004956069 txt.gz 246.2 MB
EGAF00004956070 txt.gz 244.8 MB
EGAF00004956071 txt.gz 247.5 MB
EGAF00004956072 txt.gz 97.1 MB
EGAF00004956073 txt.gz 98.1 MB
EGAF00004956074 txt.gz 128.7 MB
EGAF00004956075 txt.gz 129.8 MB
EGAF00004956076 txt.gz 45.1 MB
EGAF00004956077 txt.gz 45.4 MB
EGAF00004956078 txt.gz 72.5 MB
EGAF00004956079 txt.gz 73.2 MB
EGAF00004956080 txt.gz 87.4 MB
EGAF00004956081 txt.gz 88.1 MB
EGAF00004956082 txt.gz 78.3 MB
EGAF00004956083 txt.gz 79.1 MB
EGAF00004956084 txt.gz 56.6 MB
EGAF00004956085 txt.gz 57.0 MB
EGAF00004956086 txt.gz 58.5 MB
EGAF00004956087 txt.gz 59.0 MB
EGAF00004956088 txt.gz 73.6 MB
EGAF00004956089 txt.gz 74.4 MB
EGAF00004956090 txt.gz 46.1 MB
EGAF00004956091 txt.gz 46.6 MB
EGAF00004956092 txt.gz 111.5 MB
EGAF00004956093 txt.gz 111.3 MB
EGAF00004956094 txt.gz 118.3 MB
EGAF00004956095 txt.gz 119.3 MB
EGAF00004956096 txt.gz 120.1 MB
EGAF00004956097 txt.gz 121.2 MB
EGAF00004956098 txt.gz 200.7 MB
EGAF00004956099 txt.gz 202.4 MB
EGAF00004956100 txt.gz 49.0 MB
EGAF00004956101 txt.gz 49.4 MB
EGAF00004956102 txt.gz 231.5 MB
EGAF00004956103 txt.gz 233.9 MB
EGAF00004956104 txt.gz 46.9 MB
EGAF00004956105 txt.gz 47.4 MB
EGAF00004956106 txt.gz 127.3 MB
EGAF00004956107 txt.gz 128.5 MB
EGAF00004956108 txt.gz 62.7 MB
EGAF00004956109 txt.gz 63.4 MB
EGAF00004956110 txt.gz 203.2 MB
EGAF00004956111 txt.gz 204.8 MB
EGAF00004956112 txt.gz 57.7 MB
EGAF00004956113 txt.gz 58.1 MB
EGAF00004956114 txt.gz 125.7 MB
EGAF00004956115 txt.gz 127.1 MB
EGAF00004956116 txt.gz 317.9 MB
EGAF00004956117 txt.gz 320.2 MB
EGAF00004956118 txt.gz 29.7 MB
EGAF00004956119 txt.gz 30.1 MB
EGAF00004956120 txt.gz 54.0 MB
EGAF00004956121 txt.gz 54.5 MB
EGAF00004956122 txt.gz 99.4 MB
EGAF00004956123 txt.gz 100.2 MB
EGAF00004956124 txt.gz 152.6 MB
EGAF00004956125 txt.gz 154.3 MB
EGAF00004956126 txt.gz 207.0 MB
EGAF00004956127 txt.gz 208.7 MB
EGAF00004956128 txt.gz 143.7 MB
EGAF00004956129 txt.gz 144.9 MB
EGAF00004956130 txt.gz 152.4 MB
EGAF00004956131 txt.gz 153.5 MB
EGAF00004956132 txt.gz 198.5 MB
EGAF00004956133 txt.gz 200.7 MB
EGAF00004956134 txt.gz 136.9 MB
EGAF00004956135 txt.gz 137.9 MB
EGAF00004956136 txt.gz 243.6 MB
EGAF00004956137 txt.gz 245.2 MB
EGAF00004956138 txt.gz 168.6 MB
EGAF00004956139 txt.gz 170.3 MB
EGAF00004956140 txt.gz 36.3 MB
EGAF00004956141 txt.gz 36.6 MB
EGAF00004956142 txt.gz 40.4 MB
EGAF00004956143 txt.gz 40.9 MB
EGAF00004956144 txt.gz 170.0 MB
EGAF00004956145 txt.gz 171.8 MB
EGAF00004956146 txt.gz 36.1 MB
EGAF00004956147 txt.gz 36.3 MB
EGAF00004956148 txt.gz 271.2 MB
EGAF00004956149 txt.gz 273.4 MB
EGAF00004956150 txt.gz 242.6 MB
EGAF00004956151 txt.gz 244.0 MB
EGAF00004956152 txt.gz 88.3 MB
EGAF00004956153 txt.gz 89.3 MB
EGAF00004956154 txt.gz 74.6 MB
EGAF00004956155 txt.gz 75.4 MB
EGAF00004956156 txt.gz 58.1 MB
EGAF00004956157 txt.gz 58.9 MB
EGAF00004956158 txt.gz 79.4 MB
EGAF00004956159 txt.gz 80.2 MB
EGAF00004956160 txt.gz 50.6 MB
EGAF00004956161 txt.gz 51.0 MB
EGAF00004956162 txt.gz 312.8 MB
EGAF00004956163 txt.gz 315.2 MB
EGAF00004956164 txt.gz 129.1 MB
EGAF00004956165 txt.gz 130.1 MB
EGAF00004956166 txt.gz 222.2 MB
EGAF00004956167 txt.gz 224.0 MB
EGAF00004956168 txt.gz 155.9 MB
EGAF00004956169 txt.gz 156.5 MB
EGAF00004956170 txt.gz 90.4 MB
EGAF00004956171 txt.gz 91.3 MB
EGAF00004956172 txt.gz 87.0 MB
EGAF00004956173 txt.gz 87.9 MB
EGAF00004956174 txt.gz 87.6 MB
EGAF00004956175 txt.gz 89.0 MB
EGAF00004956176 txt.gz 136.0 MB
EGAF00004956177 txt.gz 137.5 MB
EGAF00004956178 txt.gz 102.5 MB
EGAF00004956179 txt.gz 103.7 MB
EGAF00004956180 txt.gz 229.9 MB
EGAF00004956181 txt.gz 231.2 MB
EGAF00004956182 txt.gz 145.5 MB
EGAF00004956183 txt.gz 146.7 MB
EGAF00004956184 txt.gz 57.2 MB
EGAF00004956185 txt.gz 57.5 MB
EGAF00004956186 txt.gz 47.1 MB
EGAF00004956187 txt.gz 47.5 MB
EGAF00004956188 txt.gz 239.1 MB
EGAF00004956189 txt.gz 240.7 MB
EGAF00004956190 txt.gz 157.2 MB
EGAF00004956191 txt.gz 158.7 MB
EGAF00004956192 txt.gz 182.2 MB
EGAF00004956193 txt.gz 183.2 MB
EGAF00004956194 txt.gz 328.6 MB
EGAF00004956195 txt.gz 330.8 MB
EGAF00004956196 txt.gz 48.8 MB
EGAF00004956197 txt.gz 49.2 MB
EGAF00004956198 txt.gz 47.0 MB
EGAF00004956199 txt.gz 47.6 MB
EGAF00004956200 txt.gz 134.9 MB
EGAF00004956201 txt.gz 135.5 MB
EGAF00004956202 txt.gz 369.1 MB
EGAF00004956203 txt.gz 371.7 MB
EGAF00004956204 txt.gz 53.7 MB
EGAF00004956205 txt.gz 54.4 MB
EGAF00004956206 txt.gz 115.1 MB
EGAF00004956207 txt.gz 116.2 MB
EGAF00004956208 txt.gz 59.1 MB
EGAF00004956209 txt.gz 59.7 MB
EGAF00004956210 txt.gz 187.6 MB
EGAF00004956211 txt.gz 188.5 MB
EGAF00004956212 txt.gz 138.4 MB
EGAF00004956213 txt.gz 139.5 MB
EGAF00004956214 txt.gz 41.0 MB
EGAF00004956215 txt.gz 41.4 MB
172 Files (22.4 GB)