About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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RNA-seq of iPSC-derived hepatocyte-like cells

We performed RNA-seq on polyA-enriched mRNA isolated from the original liver biopsy tissue (Liver tissue), primary liver cells (PLC), hepatocyte-like cells (HLCs) differentiated from induced pluripotent stem cells (iPSCs), and iPSCs. RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation protocol (ref. RS-122-2101, Illumina, San Diego CA, US) and sequenced using the Illumina HiSeq2500 platform following the manufacturer’s protocol. Samples were sequenced in paired-end mode to a length of 2x76 base pairs. Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files.

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DUO:0000010
version: 2019-01-07

is restricted to

A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.

DUO:0000026
version: 2019-01-07

user specific restriction

This data use modifier indicates that use is limited to use by approved users.

DATA ACCESS AGREEMENT for the University of Basel, University Hospital of Basel - Novartis Collaboration

DATA ACCESS AGREEMENT This agreement governs the terms on which access will be granted to the transcriptomic data generated by Novartis Pharma AG Lichtstrasse 35, 4056 Basel, Switzerland, and University Hospital of Basel, University of Basel (together “Data Controllers”). 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: Data means all and any human genetic data of the Data Controllers you may access from the data base of the European Genome-phenome Archive (EGA). 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 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. Should You wish to share the Data with a third party, that third party must make a separate application for access to the Data. 6. You agree to use the Data for the approved purpose and project described in your application only; use of the data for a new purpose or project will require a new application and approval. 7. You agree to acknowledge in any work based in whole or part on the Data, the published paper from which the Data derives, the version of the data, and the role of the Data Controllers and the relevant primary collectors and their funders. 8. You accept that the Data Controllers a) bear no legal responsibility for the accuracy or comprehensiveness of the Data; and b) accept no liability for indirect, consequential, or incidental, damages or losses arising from use of the Data, or from the unavailability of, or break in access to, the Data for whatever reason. 9. You understand and acknowledge that the Data is protected by copyright and other intellectual property rights, and that duplication, except as reasonably required to carry out Your research with the Data, or sale of all or part of the Data on any media is not permitted. 10. You recognize that nothing in this agreement shall operate to transfer to the User Institution any intellectual property rights relating to the Data. The User Institution has the right to develop intellectual property based on comparisons with their own data. 11. You accept that this agreement will terminate immediately upon any breach of this agreement by You and You will be required to destroy any Data held. 12. You accept that it may be necessary for the Data Controllers or its appointed agent to alter the terms of this agreement from time to time in order to address new concerns. In this event, the Data Controllers or its appointed agent will contact You to inform You of any changes and You agree that Your continued use of the Data shall be dependent on the parties entering into a new version of the Agreement. 13. You agree that you will submit a report to the Data Controllers Data Access Committee, if requested, on completion of the agreed purpose. The Data Controllers Data Access Committee agrees to treat the report and all information, data, results, and conclusions contained within such report as confidential information belonging to the User Institution. 14. You accept that the Data is subject to laws for data protection and to rights granted thereunder to the Data Subject and that You are responsible for ensuring compliance with any such applicable law and rights claimed thereunder by the Data Subject. The Data Controllers 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. 15. This agreement shall be construed, interpreted and governed by the laws of Switzerland and shall be subject to the jurisdiction of the Courts Basel-Stadt. ? For and on behalf of User: Name of Applicant(s): Signature of Applicant(s): Date: _____________________________________ _____________________________________ _____________________________________ _____________________________________ _____________________________________ _____________________________________ _____________________________________ _____________________________________ _____________________________________ For and on behalf of User Institution: Signature of Institutional or Administrative Authority: Print name: User Institution: Date: ______________________________________ ______________________________________ ______________________________________ ______________________________________ WHEN SUBMITTING THIS DOCUMENT, PLEASE INCLUDE ALL PAGES OF THE AGREEMENT WITH THIS SIGNATURE PAGE

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
EGAS00001002676 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 Quality Report
Located in
i
EGAF00001767334 fastq.gz 1.7 GB Report
EGAF00001767335 fastq.gz 1.7 GB Report
EGAF00001767336 fastq.gz 1.7 GB Report
EGAF00001767337 fastq.gz 1.7 GB Report
EGAF00001767338 fastq.gz 1.7 GB Report
EGAF00001767339 fastq.gz 1.8 GB Report
EGAF00001767340 fastq.gz 1.7 GB Report
EGAF00001767341 fastq.gz 1.8 GB Report
EGAF00001767342 fastq.gz 1.5 GB Report
EGAF00001767343 fastq.gz 1.6 GB Report
EGAF00001767344 fastq.gz 1.5 GB Report
EGAF00001767345 fastq.gz 1.6 GB Report
EGAF00001767346 fastq.gz 1.5 GB Report
EGAF00001767347 fastq.gz 1.6 GB Report
EGAF00001767348 fastq.gz 1.5 GB Report
EGAF00001767349 fastq.gz 1.6 GB Report
EGAF00001767350 fastq.gz 1.5 GB Report
EGAF00001767351 fastq.gz 1.6 GB Report
EGAF00001767352 fastq.gz 1.5 GB Report
EGAF00001767353 fastq.gz 1.6 GB Report
EGAF00001767354 fastq.gz 1.4 GB Report
EGAF00001767355 fastq.gz 1.5 GB Report
EGAF00001767356 fastq.gz 1.5 GB Report
EGAF00001767357 fastq.gz 1.5 GB Report
EGAF00001767358 fastq.gz 1.3 GB Report
EGAF00001767359 fastq.gz 1.4 GB Report
EGAF00001767360 fastq.gz 1.3 GB Report
EGAF00001767361 fastq.gz 1.4 GB Report
EGAF00001767362 fastq.gz 1.5 GB Report
EGAF00001767363 fastq.gz 1.5 GB Report
EGAF00001767364 fastq.gz 1.5 GB Report
EGAF00001767365 fastq.gz 1.6 GB Report
EGAF00001767366 fastq.gz 1.1 GB Report
EGAF00001767367 fastq.gz 1.1 GB Report
EGAF00001767368 fastq.gz 1.1 GB Report
EGAF00001767369 fastq.gz 1.1 GB Report
EGAF00001767370 fastq.gz 1.4 GB Report
EGAF00001767371 fastq.gz 1.5 GB Report
EGAF00001767372 fastq.gz 1.5 GB Report
EGAF00001767373 fastq.gz 1.5 GB Report
EGAF00001767374 fastq.gz 1.6 GB Report
EGAF00001767375 fastq.gz 1.6 GB Report
EGAF00001767376 fastq.gz 1.6 GB Report
EGAF00001767377 fastq.gz 1.6 GB Report
EGAF00001767378 fastq.gz 1.5 GB Report
EGAF00001767379 fastq.gz 1.6 GB Report
EGAF00001767380 fastq.gz 1.5 GB Report
EGAF00001767381 fastq.gz 1.5 GB Report
EGAF00001767382 fastq.gz 1.3 GB Report
EGAF00001767383 fastq.gz 1.4 GB Report
EGAF00001767384 fastq.gz 1.3 GB Report
EGAF00001767385 fastq.gz 1.4 GB Report
EGAF00001767386 fastq.gz 1.5 GB Report
EGAF00001767387 fastq.gz 1.6 GB Report
EGAF00001767388 fastq.gz 1.5 GB Report
EGAF00001767389 fastq.gz 1.6 GB Report
EGAF00001767390 fastq.gz 1.2 GB Report
EGAF00001767391 fastq.gz 1.3 GB Report
EGAF00001767392 fastq.gz 1.2 GB Report
EGAF00001767393 fastq.gz 1.2 GB Report
EGAF00001767394 fastq.gz 1.3 GB Report
EGAF00001767395 fastq.gz 1.3 GB Report
EGAF00001767396 fastq.gz 1.3 GB Report
EGAF00001767397 fastq.gz 1.3 GB Report
EGAF00001767398 fastq.gz 1.4 GB Report
EGAF00001767399 fastq.gz 1.4 GB Report
EGAF00001767400 fastq.gz 1.4 GB Report
EGAF00001767401 fastq.gz 1.4 GB Report
EGAF00001767402 fastq.gz 1.4 GB Report
EGAF00001767403 fastq.gz 1.5 GB Report
EGAF00001767404 fastq.gz 1.5 GB Report
EGAF00001767405 fastq.gz 1.5 GB Report
EGAF00001767406 fastq.gz 1.4 GB Report
EGAF00001767407 fastq.gz 1.5 GB Report
EGAF00001767408 fastq.gz 1.4 GB Report
EGAF00001767409 fastq.gz 1.5 GB Report
EGAF00001767410 fastq.gz 1.4 GB Report
EGAF00001767411 fastq.gz 1.5 GB Report
EGAF00001767412 fastq.gz 1.4 GB Report
EGAF00001767413 fastq.gz 1.5 GB Report
EGAF00001767414 fastq.gz 1.4 GB Report
EGAF00001767415 fastq.gz 1.4 GB Report
EGAF00001767416 fastq.gz 1.4 GB Report
EGAF00001767417 fastq.gz 1.4 GB Report
EGAF00001767418 fastq.gz 1.4 GB Report
EGAF00001767419 fastq.gz 1.5 GB Report
EGAF00001767420 fastq.gz 1.4 GB Report
EGAF00001767421 fastq.gz 1.5 GB Report
EGAF00001767422 fastq.gz 1.5 GB Report
EGAF00001767423 fastq.gz 1.6 GB Report
EGAF00001767424 fastq.gz 1.5 GB Report
EGAF00001767425 fastq.gz 1.6 GB Report
EGAF00001767426 fastq.gz 1.4 GB Report
EGAF00001767427 fastq.gz 1.4 GB Report
EGAF00001767428 fastq.gz 1.4 GB Report
EGAF00001767429 fastq.gz 1.4 GB Report
96 Files (140.3 GB)