Massive parallel RNA sequencing of highly purified mesenchymal cells derived from bone marrow specimens of 45 low-risk myelodysplastic syndrome cases
Highly purified mesenchymal cells (CD45-/7AAD-/CD235a-/CD31-/CD271+/CD105+) were prospectively FACS-isolated from bone marrow specimens of 45 low-risk myelodysplastic syndrome (LRMDS) cases. Gene expression profiles (GEPs) of the 45 LRMDS have been compared to GEPs derived from likewise highly purified mesenchymal cells obtained from bone marrow specimens of healthy donors for the identification of inflammatory signatures. Additionally, an overlap in inflammatory signatures has been determined by comparing the GEPs of these 45 LRMDS cases to the GEPs of 4 Shwachman-Diamond syndrome and 3 Diamond-Blackfan anemia cases, both representing different subclasses of congenital pre-leukemia syndromes with a tendency of leukemic progression and perturbed niche compartment. Finally, the GEPs and gene expression signatures have been utilized for prognostication and the prediction of leukemic progression.
- 20/09/2016
- 45 samples
- DAC: EGAC00001000537
- Technology: Illumina HiSeq 2500
Data access policy for data sets associated with the EMC-NICHE consortium studies.
THE EMC-NICHE CONSORTIUM DATA ACCESS AGREEMENT This agreement governs the terms on which access will be granted to the genotype data generated by the EMC-NICHE (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-NICHE Consortium comprised out of the following members: Dr. Marc H.G.P. Raaijmakers, Dr. Mathijs A. Sanders, Remco Hoogenboezem and Prof. dr. Arjan A van de Loosdrecht. 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 this 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. 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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-NICHE Consortium (EMC-NICHE) 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-NICHE using the following wording "This study makes use of data generated by the EMC-NICHE Consortium. Cite the relevant primary EMC-NICHE 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 |
|---|---|---|
| EGAS00001001926 | 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 | |
|---|---|---|---|---|
| EGAF00001281624 | fastq.gz | 3.0 GB | ||
| EGAF00001281625 | fastq.gz | 3.1 GB | ||
| EGAF00001281626 | fastq.gz | 4.6 GB | ||
| EGAF00001281627 | fastq.gz | 4.5 GB | ||
| EGAF00001281628 | fastq.gz | 2.6 GB | ||
| EGAF00001281629 | fastq.gz | 2.5 GB | ||
| EGAF00001281630 | fastq.gz | 3.4 GB | ||
| EGAF00001281631 | fastq.gz | 3.4 GB | ||
| EGAF00001281632 | fastq.gz | 2.0 GB | ||
| EGAF00001281633 | fastq.gz | 2.0 GB | ||
| EGAF00001281634 | fastq.gz | 3.2 GB | ||
| EGAF00001281635 | fastq.gz | 3.2 GB | ||
| EGAF00001281636 | fastq.gz | 2.4 GB | ||
| EGAF00001281637 | fastq.gz | 2.3 GB | ||
| EGAF00001281638 | fastq.gz | 2.9 GB | ||
| EGAF00001281639 | fastq.gz | 2.9 GB | ||
| EGAF00001281640 | fastq.gz | 1.4 GB | ||
| EGAF00001281641 | fastq.gz | 1.4 GB | ||
| EGAF00001281642 | fastq.gz | 5.4 GB | ||
| EGAF00001281643 | fastq.gz | 5.4 GB | ||
| EGAF00001281644 | fastq.gz | 2.5 GB | ||
| EGAF00001281645 | fastq.gz | 2.3 GB | ||
| EGAF00001281646 | fastq.gz | 1.4 GB | ||
| EGAF00001281647 | fastq.gz | 1.5 GB | ||
| EGAF00001281648 | fastq.gz | 2.0 GB | ||
| EGAF00001281649 | fastq.gz | 2.0 GB | ||
| EGAF00001281650 | fastq.gz | 1.9 GB | ||
| EGAF00001281651 | fastq.gz | 1.8 GB | ||
| EGAF00001281652 | fastq.gz | 2.5 GB | ||
| EGAF00001281653 | fastq.gz | 2.5 GB | ||
| EGAF00001281654 | fastq.gz | 4.3 GB | ||
| EGAF00001281655 | fastq.gz | 4.3 GB | ||
| EGAF00001281656 | fastq.gz | 4.8 GB | ||
| EGAF00001281657 | fastq.gz | 4.8 GB | ||
| EGAF00001281658 | fastq.gz | 7.5 GB | ||
| EGAF00001281659 | fastq.gz | 7.6 GB | ||
| EGAF00001281660 | fastq.gz | 3.3 GB | ||
| EGAF00001281661 | fastq.gz | 3.3 GB | ||
| EGAF00001281662 | fastq.gz | 2.7 GB | ||
| EGAF00001281663 | fastq.gz | 2.7 GB | ||
| EGAF00001281664 | fastq.gz | 3.0 GB | ||
| EGAF00001281665 | fastq.gz | 3.0 GB | ||
| EGAF00001281666 | fastq.gz | 4.5 GB | ||
| EGAF00001281667 | fastq.gz | 4.5 GB | ||
| EGAF00001281668 | fastq.gz | 3.9 GB | ||
| EGAF00001281669 | fastq.gz | 3.9 GB | ||
| EGAF00001281670 | fastq.gz | 3.1 GB | ||
| EGAF00001281671 | fastq.gz | 2.9 GB | ||
| EGAF00001281672 | fastq.gz | 2.0 GB | ||
| EGAF00001281673 | fastq.gz | 2.1 GB | ||
| EGAF00001281674 | fastq.gz | 4.7 GB | ||
| EGAF00001281675 | fastq.gz | 4.6 GB | ||
| EGAF00001281676 | fastq.gz | 4.1 GB | ||
| EGAF00001281677 | fastq.gz | 4.1 GB | ||
| EGAF00001281678 | fastq.gz | 2.6 GB | ||
| EGAF00001281679 | fastq.gz | 2.6 GB | ||
| EGAF00001281680 | fastq.gz | 4.6 GB | ||
| EGAF00001281681 | fastq.gz | 4.6 GB | ||
| EGAF00001281682 | fastq.gz | 4.1 GB | ||
| EGAF00001281683 | fastq.gz | 4.1 GB | ||
| EGAF00001281684 | fastq.gz | 2.9 GB | ||
| EGAF00001281685 | fastq.gz | 2.9 GB | ||
| EGAF00001281686 | fastq.gz | 1.6 GB | ||
| EGAF00001281687 | fastq.gz | 1.6 GB | ||
| EGAF00001281688 | fastq.gz | 2.0 GB | ||
| EGAF00001281689 | fastq.gz | 2.0 GB | ||
| EGAF00001281690 | fastq.gz | 5.9 GB | ||
| EGAF00001281691 | fastq.gz | 6.0 GB | ||
| EGAF00001281692 | fastq.gz | 2.4 GB | ||
| EGAF00001281693 | fastq.gz | 2.4 GB | ||
| EGAF00001281694 | fastq.gz | 3.1 GB | ||
| EGAF00001281695 | fastq.gz | 3.1 GB | ||
| EGAF00001281696 | fastq.gz | 2.2 GB | ||
| EGAF00001281697 | fastq.gz | 2.2 GB | ||
| EGAF00001281698 | fastq.gz | 3.0 GB | ||
| EGAF00001281699 | fastq.gz | 3.0 GB | ||
| EGAF00001281700 | fastq.gz | 1.9 GB | ||
| EGAF00001281701 | fastq.gz | 1.9 GB | ||
| EGAF00001281702 | fastq.gz | 1.7 GB | ||
| EGAF00001281703 | fastq.gz | 1.8 GB | ||
| EGAF00001281704 | fastq.gz | 3.2 GB | ||
| EGAF00001281705 | fastq.gz | 3.2 GB | ||
| EGAF00001281706 | fastq.gz | 3.2 GB | ||
| EGAF00001281707 | fastq.gz | 3.2 GB | ||
| EGAF00001281708 | fastq.gz | 3.9 GB | ||
| EGAF00001281709 | fastq.gz | 3.9 GB | ||
| EGAF00001281710 | fastq.gz | 6.3 GB | ||
| EGAF00001281711 | fastq.gz | 6.2 GB | ||
| EGAF00001281712 | fastq.gz | 4.1 GB | ||
| EGAF00001281713 | fastq.gz | 4.1 GB | ||
| 90 Files (295.2 GB) | ||||