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RNA-seq of atypical 3q26 samples

RNA was isolated using phenol-chloroform extraction followed by DNase digestion or using the Qiagen Allprep DNA/RNA kit and protocol (Qiagen, #80204). cDNA synthesis was done using the SuperScript II Reverse Transcriptase kit (Invitrogen). Quantitative real-time PCR was performed by using primers as described previously13,21 on the 7500 Fast Real-time PCR System (Applied Biosystems). Relative levels of gene expression were calculated using the ΔΔCt method

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Data access agreement for data generated for the study An oncogenic enhancer-rearrangement causes concomitant deregulation of EVI1 and GATA2 in leukemia

THE ERASMUSMC-HEMA CONSORTIUM DATA ACCESS AGREEMENT This agreement governs the terms on which access will be granted to the genotype data generated by the ERASMUSMC-HEMA Consortium. In signing this agreement, You are agreeing to be bound by the terms and conditions of access set out in this agreement. For the sake of clarity, the terms of access set out in this agreement apply both to the User and the User’s Institution (as defined below). User Institution and User are referred to within the agreement as “You” and “Your” shall be construed accordingly. Definitions: Consortium means the ERASMUSMC-HEMA Consortium, i.e. Drs. Ruud Delwel, Peter Valk, Stefan Gröschel, Mathijs Sanders, Bob Löwenberg and Remco Hoogenboezem. Data means all and any human genetic data obtained from the Consortium. 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. User means a researcher whose User Institution has previously completed this Data Access Agreement and has received acknowledgement of its acceptance. Publications means, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. User Institution means the organization at which the User is employed, affiliated or enrolled. 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 from the EVI1-3q Cohort 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 relevant access committees. 5. You agree not to transfer or disclose the Data, in whole or part, or any identifiable material derived from the Data, to others, except as necessary for data/safety monitoring or programme management. Should You wish to share the Data with a collaborator outwith the same 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; use of the data for a new purpose or project will require a new application and approval. 7. 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. 8. You agree to abide by the terms outlined in the Consortium 'Publications Policy' as set out in Schedule 1. 9. You agree to acknowledge in any work based in whole or part on the Data, the published paper from which the Data derives, the version of the data, and the role of the Consortium and the relevant primary collectors and their funders. Suitable wording is provided in the Publications Policy given in Schedule 1. 10. You accept that the Consortium, 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. 11. You understand and acknowledge that the Data is protected by copyright and other intellectual property rights, 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. 12. You recognize 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. 13. 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. 14. You accept that it may be necessary for the Consortium or its appointed agent to alter the terms of this agreement from time to time in order to address new concerns. In this event, the Consortium or its appointed agent will contact You to inform You of any changes and You agree that Your continued use of the Data shall be dependent on the parties entering into a new version of the Agreement. 15. You agree that you will submit a report to the Consortium Data Access Committee, if requested, on completion of the agreed purpose. The Consortium 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. 16. You accept that the Data is protected by and subject to international laws, and that You are responsible for ensuring compliance with any such applicable law. The Consortium 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 the EAA. 17. This agreement shall be construed, interpreted and governed by the laws of the Netherlands and shall be subject to the non-exclusive jurisdiction of the Dutch courts. SCHEDULE 1 Publications Policy The primary purpose of the ERASMUSMC-HEMA Consortium (EMCH) is to accelerate efforts to identify genome sequence variants influencing major causes of human morbidity and mortality, through implementation and analysis of large-scale genome-wide association studies. Additional objectives include the development and validation of informatics and analytical solutions appropriate to the scale and nature of the project, as well as use of the data generated to answer important methodological and biological questions relevant to association studies in general, and in the Netherlands in particular. The Consortium anticipates that data generated from the project will be used by others, such as required for developing new analytical methods, in understanding patterns of polymorphism and in guiding selection of markers to map genes involved in specific diseases. Authors who use data from the project must acknowledge the EMCH using the following wording "This study makes use of data generated by the ERASMUSMC-HEMA Consortium. Cite the relevant primary EMCH publication”. Users should note that the Consortium bears no responsibility for the further analysis or interpretation of these data, over and above that published by the Consortium.

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
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
EGAF00003621954 bam 4.9 GB
EGAF00003621955 bam 4.7 GB
EGAF00003621956 bam 4.9 GB
EGAF00003621957 bam 8.1 GB
EGAF00003621958 bam 4.0 GB
EGAF00003621959 bam 6.7 GB
EGAF00003621960 bam 5.6 GB
EGAF00003621961 bam 3.5 GB
EGAF00003621962 bam 4.7 GB
EGAF00003621963 bam 6.8 GB
EGAF00003621964 bam 5.1 GB
EGAF00003621965 bam 4.9 GB
EGAF00003621966 bam 4.6 GB
EGAF00003621967 bam 4.4 GB
EGAF00003621968 bam 5.7 GB
EGAF00003621969 bam 4.2 GB
EGAF00003621970 bam 4.9 GB
EGAF00003621971 bam 4.9 GB
EGAF00003621972 bam 5.4 GB
EGAF00003621973 bam 5.1 GB
EGAF00003621974 bam 3.9 GB
EGAF00003621975 bam 4.7 GB
EGAF00003621976 bam 4.9 GB
EGAF00003621977 bam 4.9 GB
EGAF00003621978 bam 4.1 GB
EGAF00003621979 bam 4.2 GB
EGAF00003622170 bai 6.0 MB
EGAF00003622171 bai 5.6 MB
EGAF00003622172 bai 5.8 MB
EGAF00003622173 bai 8.5 MB
EGAF00003622174 bai 5.9 MB
EGAF00003622175 bai 7.7 MB
EGAF00003622176 bai 6.8 MB
EGAF00003622177 bai 6.8 MB
EGAF00003622178 bai 5.7 MB
EGAF00003622179 bai 7.9 MB
EGAF00003622180 bai 6.2 MB
EGAF00003622181 bai 7.4 MB
EGAF00003622182 bai 6.4 MB
EGAF00003622183 bai 6.4 MB
EGAF00003622184 bai 6.4 MB
EGAF00003622185 bai 6.5 MB
EGAF00003622186 bai 6.3 MB
EGAF00003622187 bai 6.8 MB
EGAF00003622188 bai 6.7 MB
EGAF00003622189 bai 6.9 MB
EGAF00003622190 bai 6.0 MB
EGAF00003622191 bai 6.3 MB
EGAF00003622192 bai 6.5 MB
EGAF00003622193 bai 7.1 MB
EGAF00003622194 bai 6.0 MB
EGAF00003622195 bai 6.5 MB
52 Files (129.4 GB)