The transition from quiescent to activated states in human hematopoietic stem cells is governed by dynamic 3D genome reorganization
To elucidate the epigenetic changes which occur when human long-term hematopoietic stem cells (LT-HSC) become activated we performed Bulk ATAC-Seq on 13 sorted bulk hematopoietic populations from cord bloodas well as single-cell ATAC-Seq upon CD34+CD38-CD45RA- cells enriched for HSC as well as CD34+/CD38+ progenitor cells both from cord blood. These studies revealed gains of chromatin accessibility around CTCF binding sites during HSPC activation, as such we additionally performed Low-C to directly profile the 3D conformation of human cord-blood derived LT-HSC and Short-term hematopoietic stem cells (ST-HSC), as well as Hi-C , ATAC-Seq and CTCF ChIP-Seq upon the OCIAML-2 cell line in which CTCF sites gained during LT-HSC activation are enriched. Finally we transduced human cord-blood LT-HSC with an shCTCF vector; in-vitro cultured LT-HSC cells harbouring shCTCF were used to perform RNA-Seq, and scATAC-Seq was performed on CD34+/CD38- human CB cells transduced with shCTCF, four weeks post xeno-transplantation into mice. Collectively these studies have helped us demonstrate the role of 3D chromatin conformation changes during human LT-HSC activation.
- 62 samples
- DAC: EGAC00001000912
- Technologies: Illumina HiSeq 2000, Illumina HiSeq 2500, NextSeq 500, unspecified
Access to data generated by UHN is made available by completing the data access agreement for review by the data access committee and will be granted to qualified investigators for appropriate use.
DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom the Data Access Committee (DAC) grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The Principal Investigator and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. University Health Network: The University Health Network (UHN) is the largest clinical and research hospital in Canada. UHN is affiliated with the University of Toronto and is a member of the Toronto Academic Health Science Network. 1. 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The User Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. The User Institution agrees not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (http://www.oecd.org/science/biotech/36198812.pdf ). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify the DAC within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the DAC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The DAC may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of the province of Ontario and PHIPA. Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for The Data Access Committee Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY
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 |
|---|---|---|
| EGAS00001004740 | Epigenetics | |
| EGAS00001004741 | Epigenetics | |
| EGAS00001004742 | Epigenetics | |
| EGAS00001004743 | Epigenetics | |
| EGAS00001004744 | Epigenetics | |
| EGAS00001004745 | RNASeq |
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 | |
|---|---|---|---|---|
| EGAF00004723944 | bam | 190.9 MB | ||
| EGAF00004723945 | bam | 190.2 MB | ||
| EGAF00004723946 | bam | 189.5 MB | ||
| EGAF00004723947 | bam | 190.1 MB | ||
| EGAF00004723948 | bam | 190.7 MB | ||
| EGAF00004723949 | bam | 189.8 MB | ||
| EGAF00004723950 | bam | 191.7 MB | ||
| EGAF00004723951 | bam | 191.6 MB | ||
| EGAF00004723952 | bam | 191.6 MB | ||
| EGAF00004723953 | bam | 191.2 MB | ||
| EGAF00004723954 | bam | 191.8 MB | ||
| EGAF00004723955 | bam | 191.4 MB | ||
| EGAF00004723956 | bam | 191.1 MB | ||
| EGAF00004723957 | fastq.gz | 5.8 GB | ||
| EGAF00004723958 | fastq.gz | 4.3 GB | ||
| EGAF00004723959 | fastq.gz | 4.2 GB | ||
| EGAF00004723960 | fastq.gz | 1.5 GB | ||
| EGAF00004723961 | fastq.gz | 3.1 GB | ||
| EGAF00004723962 | fastq.gz | 3.4 GB | ||
| EGAF00004723963 | fastq.gz | 5.7 GB | ||
| EGAF00004723964 | fastq.gz | 3.4 GB | ||
| EGAF00004723965 | fastq.gz | 4.1 GB | ||
| EGAF00004723966 | fastq.gz | 8.1 GB | ||
| EGAF00004723967 | fastq.gz | 6.2 GB | ||
| EGAF00004723968 | fastq.gz | 5.4 GB | ||
| EGAF00004723969 | fastq.gz | 7.4 GB | ||
| EGAF00004723970 | fastq.gz | 1.4 GB | ||
| EGAF00004723971 | fastq.gz | 3.3 GB | ||
| EGAF00004723972 | fastq.gz | 3.8 GB | ||
| EGAF00004723973 | fastq.gz | 5.0 GB | ||
| EGAF00004723974 | fastq.gz | 3.5 GB | ||
| EGAF00004723975 | fastq.gz | 5.0 GB | ||
| EGAF00004723976 | fastq.gz | 3.1 GB | ||
| EGAF00004723977 | fastq.gz | 2.0 GB | ||
| EGAF00004723978 | fastq.gz | 778.7 MB | ||
| EGAF00004723979 | fastq.gz | 2.5 GB | ||
| EGAF00004723980 | fastq.gz | 5.1 GB | ||
| EGAF00004723981 | fastq.gz | 2.5 GB | ||
| EGAF00004723982 | fastq.gz | 6.0 GB | ||
| EGAF00004723983 | fastq.gz | 4.6 GB | ||
| EGAF00004723984 | fastq.gz | 2.3 GB | ||
| EGAF00004723985 | fastq.gz | 6.3 GB | ||
| EGAF00004723986 | fastq.gz | 6.6 GB | ||
| EGAF00004723987 | fastq.gz | 5.5 GB | ||
| EGAF00004723988 | bam | 3.4 GB | ||
| EGAF00004723989 | bam | 3.9 GB | ||
| EGAF00004723990 | bam | 3.6 GB | ||
| EGAF00004723991 | bam | 3.1 GB | ||
| EGAF00004723992 | bam | 18.7 GB | ||
| EGAF00004723993 | bam | 26.4 GB | ||
| EGAF00004723994 | bam | 17.0 GB | ||
| EGAF00004723995 | bam | 3.0 GB | ||
| EGAF00004723996 | bam | 5.5 GB | ||
| EGAF00004723997 | fastq.gz | 2.6 GB | ||
| EGAF00004723998 | fastq.gz | 6.2 GB | ||
| EGAF00004723999 | fastq.gz | 2.4 GB | ||
| EGAF00004724000 | fastq.gz | 4.9 GB | ||
| EGAF00004724001 | fastq.gz | 2.4 GB | ||
| EGAF00004724002 | fastq.gz | 5.4 GB | ||
| EGAF00005296558 | fastq.gz | 2.7 GB | ||
| EGAF00005296559 | fastq.gz | 2.4 GB | ||
| EGAF00005296560 | fastq.gz | 4.3 GB | ||
| EGAF00005296561 | fastq.gz | 2.0 GB | ||
| EGAF00005296562 | fastq.gz | 1.7 GB | ||
| EGAF00005296563 | fastq.gz | 1.8 GB | ||
| EGAF00005296564 | fastq.gz | 1.8 GB | ||
| EGAF00005296565 | fastq.gz | 83.9 GB | ||
| EGAF00005296566 | fastq.gz | 85.2 GB | ||
| EGAF00005296567 | fastq.gz | 1.5 GB | ||
| EGAF00005296568 | fastq.gz | 1.7 GB | ||
| EGAF00005296569 | fastq.gz | 1.7 GB | ||
| EGAF00005296570 | fastq.gz | 1.8 GB | ||
| EGAF00005296571 | fastq.gz | 3.5 GB | ||
| EGAF00005296572 | fastq.gz | 3.6 GB | ||
| EGAF00005296573 | fastq.gz | 3.7 GB | ||
| EGAF00005296574 | fastq.gz | 3.8 GB | ||
| EGAF00005296575 | fastq.gz | 3.2 GB | ||
| EGAF00005296576 | fastq.gz | 3.2 GB | ||
| EGAF00005296577 | fastq.gz | 3.4 GB | ||
| EGAF00005296578 | fastq.gz | 3.5 GB | ||
| EGAF00005296579 | fastq.gz | 3.5 GB | ||
| EGAF00005296580 | fastq.gz | 3.5 GB | ||
| EGAF00005296581 | fastq.gz | 3.3 GB | ||
| EGAF00005296582 | fastq.gz | 3.5 GB | ||
| 84 Files (476.9 GB) | ||||