Need Help?

ATAC-seq of a selected group of AML cases

ATAC-seq data were generated for a number of selected patients to investigate changes in enhancer and promoter regions. ATAC-seq was essentially carried out as described in31. Briefly, prior to transposition the viability of the cells was assessed and 1 × 106 cells were treated in culture medium with DNase I (Sigma) at a final concentration of 200 U ml−1 for 30 minutes at 37 °C. After Dnase I treatment, cells were washed twice with ice-cold PBS, and cell viability and the corresponding cell count were assessed. 5 × 104 cells were aliquoted into a new tube and spun down at 500 × g for 5 minutes at 4 °C, before the supernatant was discarded completely. The cell pellet was resuspended in 50 µl of ATAC-RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20, and 1% Digitonin (Promega), and was incubated on ice for 3 minutes to lyse the cells. Lysis was washed out with 1 ml of ATAC-RSB buffer containing 0.1% Tween-20. Nuclei were pelleted at 500 × g for 10 minutes at 4 °C. The supernatant was discarded carefully and the cell pellet was resuspended in 50 µl of transposition mixture (25 µl 2× tagment DNA buffer, 2.5 µl transposase (100 nM final; Illumina), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O) by pipetting up and down six times. The reaction was incubated at 37 °C for 30 minutes with mixing before the DNA was purified using the Monarch PCR & DNA Cleanup Kit (NEB) according to the manufacturer’s instructions. Purified DNA was eluted in 20 µl elution buffer (EB) and 10 µl purified sample was objected to a ten-cycle PCR amplification using Nextera i7- and i5-index primers (Illumina). Purification and size selection of the amplified DNA were carried out with Agencourt AMPure XP beads. For purification the ratio of sample to beads was set to 1:1.8, whereas for size selection the ratio was set to 1:0.55. Purified samples were eluted in 15 µl of EB. Quality and concentration of the generated ATAC libraries were analyzed using the High Sensitivity D1000 ScreenTape Kit (Agilent) and libraries were sequenced paired-end on a NovaSeq (Illumina). ATAC-seq reads were aligned to the human reference genome build hg19 with bowtie2

Request Access

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. You agree to delete the data from your computers after a period of 2 years, unless an extension request is submitted to the DAC. 18. 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
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
EGAF00005209454 1619368473945 888.5 MB
EGAF00005209455 bam 462.7 MB
EGAF00005209456 1619369491031 2.3 GB
EGAF00005209457 1619369433092 2.6 GB
EGAF00005209458 1619368232319 2.5 GB
EGAF00005209459 1619370554614 2.6 GB
EGAF00005209460 1619368473945 1.9 GB
EGAF00005209461 1619369491031 3.1 GB
EGAF00005209462 1619367768830 2.6 GB
EGAF00005209463 1619369977098 2.8 GB
EGAF00005209464 1619368510768 1.1 GB
EGAF00005209465 1619368171711 923.2 MB
EGAF00005209466 1619367911637 542.2 MB
EGAF00005209467 1619370554615 2.8 GB
EGAF00005209468 bam 438.6 MB
EGAF00005209469 1619367850942 2.8 GB
EGAF00005209470 1619367768830 1.2 GB
EGAF00005209471 1619367452624 590.4 MB
EGAF00005209472 1619368393824 623.1 MB
EGAF00005209473 1619369977098 2.6 GB
EGAF00005209474 bam 411.0 MB
EGAF00005209475 bam 415.1 MB
EGAF00005209476 1619367768830 2.7 GB
EGAF00005209477 1619367569853 624.9 MB
EGAF00005209478 1619368107661 2.3 GB
EGAF00005209479 1628272918587 2.3 GB
EGAF00005209480 1628274215805 1.9 GB
EGAF00005209481 1628272918587 2.2 GB
EGAF00005209482 1628272918587 902.6 MB
EGAF00005209483 1628274215805 1.7 GB
EGAF00005209484 1628272918587 2.1 GB
EGAF00005209485 1628274215805 2.0 GB
EGAF00005209486 1628272918587 1.7 GB
EGAF00005209487 1628272918587 1.7 GB
EGAF00005209488 1628272918587 877.7 MB
EGAF00005209489 1628272918587 646.4 MB
EGAF00005209490 1628272918587 1.8 GB
EGAF00005209491 1628272918587 844.2 MB
EGAF00005209492 1628272918587 831.2 MB
EGAF00005209493 1628272918587 2.1 GB
EGAF00005209494 1628272918587 857.4 MB
EGAF00005209495 1628272918587 833.9 MB
EGAF00005209496 1628272918587 847.4 MB
EGAF00005209497 bam 497.2 MB
EGAF00005209498 1628272918587 1.1 GB
EGAF00005209499 1628271462688 548.7 MB
EGAF00005209500 1628272918587 1.4 GB
EGAF00005209501 1628272918587 569.7 MB
EGAF00005209502 1628274215805 4.0 GB
EGAF00005209503 bam 418.9 MB
EGAF00005209504 1628272918587 554.3 MB
EGAF00005209505 1628274215805 2.0 GB
EGAF00005209506 1628272918587 1.2 GB
EGAF00005209507 1628272918587 2.2 GB
EGAF00005209508 1628272918587 2.3 GB
EGAF00005209509 1628274215804 3.9 GB
EGAF00005209510 1628274215805 1.7 GB
EGAF00005209511 1628272918587 1.4 GB
EGAF00005209512 1628272918587 2.0 GB
EGAF00005209513 1628274215805 2.2 GB
EGAF00005209514 1628272918587 5.2 GB
EGAF00005209515 1628274215805 2.9 GB
EGAF00005209516 1628272918587 2.7 GB
EGAF00005209517 1628274215805 2.3 GB
64 Files (109.0 GB)