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. 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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 |
|---|---|---|
| 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) | ||||