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H3K27ac ChIP-seq in a selected group of AML patients

ChIP-seq data were generated for a number of selected patients to investigate changes in enhancer and promoter regions. ChIP was performed as described previously with slight modifications27. Briefly, cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature and the reaction was quenched with glycine at a final concentration of 0.125 M. Chromatin was sheared using the Covaris S220 focused-ultrasonicator to an average size of 250–350 bp. A total of 2.5 µg of antibody against H3K27ac (Abcam, ab4729) was added to sonicated chromatin of 2 × 106 cells and incubated overnight at 4 °C. Protein A sepharose beads (GE healthcare) were added to the ChIP reactions and incubated for 2 h at 4 °C. Beads were washed and chromatin was eluted. After crosslink reversal, RNase A and proteinase K treatment, DNA was extracted with the Monarch PCR & DNA Cleanup kit (NEB). Sequencing libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. The quality of dsDNA libraries was analyzed using the High Sensitivity D1000 ScreenTape Kit (Agilent) and concentrations were assessed with the Qubit dsDNA HS Kit (Thermo Fisher Scientific). Libraries were single-end sequenced on a HiSeq 4000 (Illumina). ChIP-seq reads were aligned to the human reference genome build hg19 with bowtie

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Data access policy of the EMC-HEMA-AML consortium for adult acute myeloid leukemia data

THE EMC-HEMA-AML CONSORTIUM DATA ACCESS AGREEMENT This agreement governs the terms on which access will be granted to the genotype data generated by the EMC-HEMA-AML (part of the ERASMUSMC-HEMA consortium) 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 EMC-HEMA-AML Consortium comprised out of the following members: Dr. Bas Wouters, Dr. Ruud Delwel, Roger Mulet-Lázaro, Dr. Mathijs A. Sanders, Dr. Peter J.M. Valk, 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. Acute Myeloid Leukemia is hereafter referred to within the agreement as "AML". 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 adult ALL 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. The relevant access committess will see to it that the Data is not used in publications outside the project described in the original application. 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 EMC-HEMA-AML Consortium 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 EMC-HEMA-AML using the following wording "This study makes use of data generated by the EMC-HEMA-AML Consortium. Cite the relevant primary EMC-HEMA-AML 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
EGAS00001004684 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
EGAF00005209101 bam 2.8 GB
EGAF00005209102 bam 2.3 GB
EGAF00005209103 bam 2.0 GB
EGAF00005209104 bam 1.6 GB
EGAF00005209105 bam 2.6 GB
EGAF00005209106 bam 1.1 GB
EGAF00005209107 bam 1.9 GB
EGAF00005209108 bam 1.2 GB
EGAF00005209109 bam 924.7 MB
EGAF00005209110 bam 1.1 GB
EGAF00005209111 bam 1.3 GB
EGAF00005209112 bam 840.5 MB
EGAF00005209113 bam 1.1 GB
EGAF00005209114 bam 370.1 MB
EGAF00005209115 bam 892.0 MB
EGAF00005209116 bam 1.1 GB
EGAF00005209117 bam 975.9 MB
EGAF00005209118 bam 887.0 MB
EGAF00005209119 bam 946.8 MB
EGAF00005209120 bam 1.3 GB
EGAF00005209121 bam 1.9 GB
EGAF00005209122 bam 920.6 MB
EGAF00005209123 bam 5.5 GB
EGAF00005209124 bam 712.2 MB
EGAF00005209125 bam 1.4 GB
EGAF00005209126 bam 4.6 GB
EGAF00005209127 bam 1.9 GB
EGAF00005209128 bam 3.1 GB
EGAF00005209129 bam 807.4 MB
EGAF00005209130 bam 1.7 GB
EGAF00005209131 bam 717.7 MB
EGAF00005209132 bam 1.6 GB
EGAF00005209133 bam 1.8 GB
EGAF00005209134 bam 1.2 GB
EGAF00005209135 bam 1.3 GB
EGAF00005209136 bam 1.3 GB
EGAF00005209137 bam 1.9 GB
EGAF00005209138 bam 1.2 GB
EGAF00005209139 bam 943.0 MB
EGAF00005209140 bam 1.0 GB
EGAF00005209141 bam 1.2 GB
EGAF00005209142 bam 1.1 GB
EGAF00005209143 bam 1.4 GB
EGAF00005209144 bam 837.0 MB
EGAF00005209145 bam 1.2 GB
EGAF00005209146 bam 1.3 GB
EGAF00005209147 bam 971.9 MB
EGAF00005209148 bam 1.0 GB
EGAF00005209149 bam 1.3 GB
EGAF00005209150 bam 1.4 GB
EGAF00005209151 bam 2.1 GB
EGAF00005209152 bam 917.4 MB
EGAF00005209153 bam 1.4 GB
EGAF00005209154 bam 939.9 MB
EGAF00005209155 bam 968.8 MB
EGAF00005209156 bam 4.3 GB
EGAF00005209157 bam 1.2 GB
EGAF00005209158 bam 1.1 GB
EGAF00005209159 bam 873.7 MB
EGAF00005209160 bam 1.0 GB
EGAF00005209161 bam 2.4 GB
EGAF00005209162 bam 653.5 MB
EGAF00005209163 bam 2.2 GB
EGAF00005209164 bam 3.8 GB
EGAF00005209165 bam 1.3 GB
EGAF00005209166 bam 4.0 GB
EGAF00005209167 bam 972.6 MB
EGAF00005209168 bam 631.8 MB
EGAF00005209169 bam 820.8 MB
EGAF00005209170 bam 1.1 GB
EGAF00005209171 bam 1.1 GB
EGAF00005209172 bam 1.1 GB
EGAF00005209173 bai 6.3 MB
EGAF00005209174 bai 6.7 MB
EGAF00005209179 bai 7.5 MB
EGAF00005209182 bai 7.2 MB
EGAF00005209183 bai 6.5 MB
EGAF00005209186 bai 7.0 MB
EGAF00005209188 bai 6.7 MB
EGAF00005209200 bai 6.7 MB
EGAF00005209203 bai 6.4 MB
EGAF00005209206 bai 6.3 MB
EGAF00005209207 bai 6.8 MB
EGAF00005209209 bai 6.5 MB
EGAF00005209213 bai 6.8 MB
EGAF00005209218 bai 6.4 MB
EGAF00005209222 bai 6.7 MB
EGAF00005209227 bai 6.6 MB
EGAF00005209228 bai 7.9 MB
EGAF00005209234 bai 6.9 MB
EGAF00005209235 bai 6.4 MB
EGAF00005209237 bai 6.4 MB
EGAF00005209238 bai 7.6 MB
EGAF00005209239 bai 6.9 MB
EGAF00005209247 bai 6.3 MB
EGAF00005209248 bai 6.6 MB
EGAF00005209258 bai 6.5 MB
EGAF00005209259 bai 6.8 MB
EGAF00005209263 bai 6.5 MB
EGAF00005209264 bai 6.5 MB
EGAF00005209267 bai 6.6 MB
EGAF00005209272 bai 6.8 MB
EGAF00005209276 bai 6.3 MB
EGAF00005209281 bai 6.4 MB
EGAF00005209283 bai 6.4 MB
EGAF00005209291 bai 6.9 MB
EGAF00005209295 bai 6.7 MB
EGAF00005209296 bai 6.7 MB
EGAF00005209300 bai 6.5 MB
EGAF00005209303 bai 6.6 MB
EGAF00005209308 bai 6.0 MB
EGAF00005209313 bai 6.8 MB
EGAF00005209315 bai 7.8 MB
EGAF00005209317 bai 6.6 MB
EGAF00005209319 bai 6.7 MB
EGAF00005209320 bai 7.1 MB
EGAF00005209324 bai 6.3 MB
EGAF00005209327 bai 6.9 MB
EGAF00005209331 bai 6.5 MB
EGAF00005209333 bai 6.6 MB
EGAF00005209336 bai 6.3 MB
EGAF00005209346 bai 6.3 MB
EGAF00005209353 bai 6.4 MB
EGAF00005209364 bai 6.2 MB
EGAF00005209367 bai 6.4 MB
EGAF00005209368 bai 7.3 MB
EGAF00005209369 bai 6.9 MB
EGAF00005209373 bai 6.4 MB
EGAF00005209375 bai 7.1 MB
EGAF00005209376 bai 6.5 MB
EGAF00005209386 bai 6.3 MB
EGAF00005209387 bai 7.7 MB
EGAF00005209388 bai 6.7 MB
EGAF00005209394 bai 6.8 MB
EGAF00005209395 bai 6.6 MB
EGAF00005209396 bai 6.3 MB
EGAF00005209405 bai 6.9 MB
EGAF00005209410 bai 6.3 MB
EGAF00005209413 bai 7.3 MB
EGAF00005209417 bai 6.3 MB
EGAF00005209418 bai 6.7 MB
EGAF00005209419 bai 6.3 MB
EGAF00005209437 bai 6.4 MB
EGAF00005209453 bai 6.7 MB
144 Files (109.6 GB)