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RNA-seq of cultured human hematopoietic stem and progenitor cells from umblical cord blood in cytokine-rich ex vivo culture conditions following sphingolipid modulation

In order to elucidate the biological pathways altered by sphingolipid modulation with N-(4-hydroxyphenyl) retinamide (4HPR) treatment in human HSPC that may contribute to the restraint in proliferation while promoting persistence of HSC self-renewal, as well as determine the mechanism of synergy in enhancement of HSC self-renewal with CB CD34+ agonists UM171 and StemRegenin 1 (SR1), we performed RNA-sequencing (RNA-Seq) of 3 pools of lin-CB cells following 2 or 4 days with DMSO, 4HPR, UM171+SR1 or 3-Factor (4HPR+UM171+SR1). We identified modulation of sphingolipid metabolism regulates self-renewal through activating coordinated stress pathways that coalesce on endoplasmic reticulum stress and autophagy programs.

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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. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. 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
EGAS00001003756 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
EGAF00002538846 fastq.gz 2.5 GB
EGAF00002538847 fastq.gz 2.6 GB
EGAF00002538848 fastq.gz 2.5 GB
EGAF00002538849 fastq.gz 2.6 GB
EGAF00002538850 fastq.gz 2.6 GB
EGAF00002538851 fastq.gz 2.7 GB
EGAF00002538852 fastq.gz 2.6 GB
EGAF00002538853 fastq.gz 2.7 GB
EGAF00002538854 fastq.gz 2.6 GB
EGAF00002538855 fastq.gz 2.6 GB
EGAF00002538856 fastq.gz 2.5 GB
EGAF00002538857 fastq.gz 2.6 GB
EGAF00002538858 fastq.gz 2.4 GB
EGAF00002538859 fastq.gz 2.4 GB
EGAF00002538860 fastq.gz 2.4 GB
EGAF00002538861 fastq.gz 2.4 GB
EGAF00002538862 fastq.gz 2.4 GB
EGAF00002538863 fastq.gz 2.4 GB
EGAF00002538864 fastq.gz 2.4 GB
EGAF00002538865 fastq.gz 2.4 GB
EGAF00002538866 fastq.gz 1.4 GB
EGAF00002538867 fastq.gz 1.4 GB
EGAF00002538868 fastq.gz 1.4 GB
EGAF00002538869 fastq.gz 1.4 GB
EGAF00002538870 fastq.gz 1.4 GB
EGAF00002538871 fastq.gz 1.4 GB
EGAF00002538872 fastq.gz 2.4 GB
EGAF00002538873 fastq.gz 2.4 GB
EGAF00002538874 fastq.gz 2.4 GB
EGAF00002538875 fastq.gz 2.4 GB
EGAF00002538876 fastq.gz 2.3 GB
EGAF00002538877 fastq.gz 2.3 GB
EGAF00002538878 fastq.gz 2.3 GB
EGAF00002538879 fastq.gz 2.3 GB
EGAF00002538880 fastq.gz 2.5 GB
EGAF00002538881 fastq.gz 2.5 GB
EGAF00002538882 fastq.gz 2.5 GB
EGAF00002538883 fastq.gz 2.5 GB
EGAF00002538884 fastq.gz 1.7 GB
EGAF00002538885 fastq.gz 1.7 GB
EGAF00002538886 fastq.gz 1.7 GB
EGAF00002538887 fastq.gz 1.7 GB
EGAF00002538888 fastq.gz 1.7 GB
EGAF00002538889 fastq.gz 1.7 GB
EGAF00002538890 fastq.gz 1.6 GB
EGAF00002538891 fastq.gz 1.7 GB
EGAF00002538892 fastq.gz 1.6 GB
EGAF00002538893 fastq.gz 1.7 GB
EGAF00002538894 fastq.gz 1.6 GB
EGAF00002538895 fastq.gz 1.7 GB
EGAF00002538896 fastq.gz 1.8 GB
EGAF00002538897 fastq.gz 1.8 GB
EGAF00002538898 fastq.gz 1.8 GB
EGAF00002538899 fastq.gz 1.8 GB
EGAF00002538900 fastq.gz 1.8 GB
EGAF00002538901 fastq.gz 1.8 GB
EGAF00002538902 fastq.gz 1.7 GB
EGAF00002538903 fastq.gz 1.7 GB
EGAF00002538904 fastq.gz 1.7 GB
EGAF00002538905 fastq.gz 1.7 GB
EGAF00002538906 fastq.gz 1.7 GB
EGAF00002538907 fastq.gz 1.7 GB
EGAF00002538908 fastq.gz 1.6 GB
EGAF00002538909 fastq.gz 1.6 GB
EGAF00002538910 fastq.gz 1.6 GB
EGAF00002538911 fastq.gz 1.6 GB
EGAF00002538912 fastq.gz 1.6 GB
EGAF00002538913 fastq.gz 1.6 GB
EGAF00002538914 fastq.gz 1.7 GB
EGAF00002538915 fastq.gz 1.7 GB
EGAF00002538916 fastq.gz 1.7 GB
EGAF00002538917 fastq.gz 1.7 GB
EGAF00002538918 fastq.gz 1.7 GB
EGAF00002538919 fastq.gz 1.7 GB
EGAF00002538920 fastq.gz 1.8 GB
EGAF00002538921 fastq.gz 1.8 GB
EGAF00002538922 fastq.gz 1.8 GB
EGAF00002538923 fastq.gz 1.8 GB
EGAF00002538924 fastq.gz 1.7 GB
EGAF00002538925 fastq.gz 1.8 GB
EGAF00002538926 fastq.gz 1.8 GB
EGAF00002538927 fastq.gz 1.8 GB
EGAF00002538928 fastq.gz 1.8 GB
EGAF00002538929 fastq.gz 1.8 GB
EGAF00002538930 fastq.gz 1.8 GB
EGAF00002538931 fastq.gz 1.8 GB
EGAF00002538932 fastq.gz 1.8 GB
EGAF00002538933 fastq.gz 1.8 GB
EGAF00002538934 fastq.gz 1.7 GB
EGAF00002538935 fastq.gz 1.8 GB
EGAF00002538936 fastq.gz 1.7 GB
EGAF00002538937 fastq.gz 1.8 GB
EGAF00002538938 fastq.gz 1.7 GB
EGAF00002538939 fastq.gz 1.7 GB
EGAF00002538940 fastq.gz 1.7 GB
EGAF00002538941 fastq.gz 1.7 GB
EGAF00002538942 fastq.gz 1.7 GB
EGAF00002538943 fastq.gz 1.7 GB
EGAF00002538944 fastq.gz 1.6 GB
EGAF00002538945 fastq.gz 1.6 GB
EGAF00002538946 fastq.gz 1.6 GB
EGAF00002538947 fastq.gz 1.6 GB
EGAF00002538948 fastq.gz 1.6 GB
EGAF00002538949 fastq.gz 1.6 GB
EGAF00002538950 fastq.gz 1.7 GB
EGAF00002538951 fastq.gz 1.7 GB
EGAF00002538952 fastq.gz 1.7 GB
EGAF00002538953 fastq.gz 1.7 GB
EGAF00002538954 fastq.gz 1.7 GB
EGAF00002538955 fastq.gz 1.7 GB
EGAF00002538956 fastq.gz 2.4 GB
EGAF00002538957 fastq.gz 2.5 GB
EGAF00002538958 fastq.gz 2.4 GB
EGAF00002538959 fastq.gz 2.5 GB
EGAF00002538960 fastq.gz 1.9 GB
EGAF00002538961 fastq.gz 1.9 GB
EGAF00002538962 fastq.gz 1.9 GB
EGAF00002538963 fastq.gz 1.9 GB
EGAF00002538964 fastq.gz 1.9 GB
EGAF00002538965 fastq.gz 1.9 GB
EGAF00002538966 fastq.gz 1.7 GB
EGAF00002538967 fastq.gz 1.7 GB
EGAF00002538968 fastq.gz 1.6 GB
EGAF00002538969 fastq.gz 1.6 GB
EGAF00002538970 fastq.gz 1.6 GB
EGAF00002538971 fastq.gz 1.6 GB
EGAF00002538972 fastq.gz 2.8 GB
EGAF00002538973 fastq.gz 2.8 GB
EGAF00002538974 fastq.gz 2.8 GB
EGAF00002538975 fastq.gz 2.8 GB
130 Files (252.8 GB)