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Chromatin accessibility analysis of hepatocyte-like cell in vitro differentiation from iPSC in comparison to primary human hepatocytes

Fastq files of ATAC-seq data of induced pluripotent stem cells (iPSC), definitive endoderm (DE), hepatocyte-like cells (HLC) and primary human hepatocytes (PHH). The dataset comprises data from two different in vitro differentiation protocols: Cellartis (Takara Bio, "CEL", n = 4) and as described by Wang et al. (PMID: 28287600, "HAY", n = 1), as well as from 3 PHH donors.

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StemNet Data Access Agreement

StemNet Data Access Agreement This agreement governs the terms on which access will be granted to the controlled access datasets generated by the StemNet Project. By 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 to the User’s Institution (as defined below). Definitions: Data Producer: A member of the StemNet project. External Collaborator: A collaborator of the User, working for an institution other than the User Institution(s). StemNet Data: The controlled access data of generated within the StemNet project. Human Donor: An individual having contributed their personal data/biomaterial to StemNet. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. User: An applicant (principal investigator), having signed this Data Access Agreement, whose User Institution has co-signed this Data Access Agreement, both of them having received acknowledgment of its acceptance. User Institution(s): Institution(s) at which the User is employed, affiliated or enrolled. A representative of it has co-signed this data Access Agreement with the User and received acknowledgment of its acceptance. Terms and Conditions: In signing this Agreement: 1. The User and the User Institution(s) agree to only use the StemNet Data for the objectives and analyses outlined in section E “Scientific abstract” and as approved by their ethics committee(s) in the letter requested in section I “Research ethics” of the Data Access Application form (if so required). Use of the StemNet Data for a new purpose or project will require a new application and approval. 2. The User and the User Institution(s) agree that the StemNet Data are made available for one (1) year. The User and the User Institution(s) agree to destroy/discard any StemNet Data held once it is no longer used for the project described in section E “Scientific abstract” of the Data Access Application Form or after the end of the granted time-period of one year unless obligated to retain the StemNet Data for archival purposes in conformity with national audits or legal requirements. To extend the use of StemNet Data after the one-year period, Users and User Institution(s) must re-apply to access the data. 3. The User and the User Institution(s) agree to preserve, at all times, the confidentiality of the information and StemNet Data. In particular, they undertake not to use, or attempt to use the StemNet Data to compromise or otherwise infringe the confidentiality of information on Human Donors. 4. 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The User and the User Institution(s) agree not to transfer or disclose the StemNet Data, in whole or part, or any material derived from the StemNet Data, to anyone not listed in sections A “Name of applicant (principal investigator), including affiliations and contact details“ and B “Name of authorized personnel within your institution, including affiliations and contact details.“ of the Data Access Application form, except as necessary for data safety monitoring, national audits or program management. Should the User or the User Institution(s) wish to share the StemNet Data with an External Collaborator, the External Collaborator must complete a separate application for Access to the StemNet Data. 7. The User and the User Institution(s) accept that the original Data Producers, or copyright holders, or the funders of the StemNet Data or any part of the StemNet Data supplied: a) bear no legal responsibility for accuracy or comprehensiveness of the StemNet Data b) accept no liability for indirect, consequential, or incidental, damages or losses arising from use of the StemNet Data, or from the unavailability of, interruption in StemNet Data access for whatever reason c) bear no responsibility for the further analysis or interpretation of these StemNet Data, over and above that published by the Data Producers. 8. The User and the User Institution(s) agree that they have the secure computation infrastructure and expertise to analyse the StemNet Data. 9. The User and the User Institution(s) agree to follow the IHEC publication policy as outlined in section E.5 of IHEC goals, structure, policies and guidelines (Version Jan 2013, http://ihec-epigenomes.org/about/policies-and-guidelines/). This includes respecting the moratorium period of one year from the time of data release, thus agreeing that you will not use the StemNet Data in a Publication before the end of this nine-month period, or until the StemNet Data is published by the Data Producers, whichever occurs first. 10. The User and the User Institution(s) agree to recognize the contribution of the Data Producers and to include a proper acknowledgement in any work based in whole or part on the StemNet Data. 11. The User and the User Institution(s) accept that StemNet Data may be reissued from time to time, with suitable versioning. If the reissue is at the request of ethical scrutiny, the User and the User Institution(s) will destroy earlier versions of the data. 12. The User and the User Institution(s) agree not to make intellectual property claims on the StemNet Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of the StemNet data, or conclusions drawn directly from the StemNet Data. 13. The User and the User Institution(s) can elect to perform further research that would add intellectual and resource capital to the StemNet Data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User and the User Institution(s) agree to implement licensing policies that will not obstruct further research and to follow a national guideline that is in conformity with the OECD, “Guidelines for the Licensing of the Genetic Inventions”. 14. The User and the User Institution(s) will update the list of authorized personnel (section B in the Data Access Application form) to reflect any changes in researchers, collaborators and personnel within 30 days of the changes made. This update can be sent by email to the DAC. 15. The User and the User Institution(s) must notify the StemNet DAC prior to any significant change to the research protocol of the User. This update can be sent by email to the DAC. 16. The User and the User Institution(s) will notify the StemNet DAC as soon as they become aware of a breach of the terms or conditions of this agreement. 17. The User and the User Institution(s) accept that this agreement may terminate upon any breach of this agreement from the User, the User Institution(s) or any authorized personnel mentioned in section B “Name of authorized personnel within your institution, including affiliations and contact details“ of the Data Access Application form. In this case, the User and the User Institution(s) will be required to destroy/discard any StemNet Data held, including copies and backup copies. This clause does not prevent the User or the User Institution(s) from retaining the StemNet Data for archival purposes in conformity with national audits or legal requirements. 18. The User and the User Institution(s) accept that it may be necessary for the Data Producers or its appointed agent to alter the terms of this agreement from time to time. In this event, the Data Producers or their appointed agent will contact the User and the User Institution(s) to inform them of any changes. 19. If requested, the User and the User Institution(s) will allow data security and management documentation to be inspected to verify that they are complying with the terms of this Data Access Agreement. 20. The User and the User Institution(s) agree to distribute a copy of this agreement and explain its content to any person mentioned in section B “Name of authorized personnel within your institution, including affiliations and contact details“ of the Data Access Application form. 0 I have read the policies and guidelines of the International Human Epigenome Consortium (http://ihec-epigenomes.org/about/policies-and-guidelines/). Applicant: Name: Signed: Date: Authorized institutional representative: Name: Signed: Date: The completed agreement must be sent by email to the DAC (hengstler@ifado.de and j.walter@mx.uni-saarland.de).

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
EGAS00001004201 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
EGAF00003297122 fastq.gz 1.8 GB
EGAF00003297123 fastq.gz 1.5 GB
EGAF00003297125 fastq.gz 2.2 GB
EGAF00003297126 fastq.gz 1.9 GB
EGAF00003297127 fastq.gz 1.9 GB
EGAF00003297128 fastq.gz 2.1 GB
EGAF00003297129 fastq.gz 1.8 GB
EGAF00003297130 fastq.gz 3.1 GB
EGAF00003297131 fastq.gz 2.6 GB
EGAF00003297132 fastq.gz 2.7 GB
EGAF00003297133 fastq.gz 2.8 GB
EGAF00003297134 fastq.gz 2.3 GB
EGAF00003297135 fastq.gz 1.7 GB
EGAF00003297138 fastq.gz 1.9 GB
EGAF00003297139 fastq.gz 2.1 GB
15 Files (32.3 GB)