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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MPNST study - Spatial data

10X Visium spatial transcriptomic data of one MPNST patient

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Francis Crick - Data Access Agreement

Francis Crick - Data Access Agreement - General Anon [Note: This agreement is provided as an example of the terms we ask data users to adhere to. The final agreement we issue may vary from the terms specified below.] [Section 2] These terms and conditions govern access to the managed access datasets (set out in Section 3) to which the Data Recipient has requested access. The Data Recipient agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the Data Recipient to whom the Crick grants access to the Data, all of whom shall be employees of the Data Recipient or registered students at the Data Recipient. This includes the User, the initial individuals listed in Section 1 and any other individuals for whom the Data Recipient subsequently requests access to the Data. Crick: The Francis Crick Institute Limited, a registered charity in England and Wales (no. 1140062) and a company registered in England and Wales (no. 06885462), whose address is at 1 Midland Road, London, NW1 1AT, and who is making the Data available. Data: The managed access datasets to which the Data Recipient has requested access. Data Producers: The Crick and any collaborators listed in Section 3 responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the Data Recipient, working for an institution other than the Data Recipient. Principal Investigator: The principal investigator for the Project as set out in Section 1. Project: The project for which the Data Recipient has requested access to these Data. A description of the Project is set out in Section 1. 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: 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. Data Recipient(s): The institution that has requested access to the Data, as set out in Section 1. 1. The Data Recipient agrees to only use these Data: a) for the purpose and duration of the Project (described in Section 1); b) for Research Purposes; c) at the address in Section 1; d) in accordance with all applicable laws, regulations and ethical requirements, including without limitation applicable laws on data protection; and e) for Research Purposes which are within the limitations (if any) set out in Section 3. Any use of the Data for another research field or area will need to be approved under a new agreement. 2. The Data Recipient agrees to preserve, at all times, the confidentiality of these Data. It undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. The Data Recipient agrees to use at least the measures set out in Section 3 to protect these Data. 3. The Data Recipient 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 Data Recipient agrees not to link or combine these Data to other information or archived data available, or analyse or make any use of any Data in a way that could, or has the potential to, re-identify the Research Participants, even if access to that data has been formally granted to the Data Recipient or is freely available without restriction. 5. The Data Recipient agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. If the employment/ affiliation of any Authorised Personnel with the Data Recipient ends, or the Authorised Personnel’s professional responsibilities no longer require access to the Data, or the scope of required access changes, the Data Recipient shall ensure that such Authorised Personnel Data access is revoked or changed appropriately. If such access is not changed in a timely manner, the Data Recipient shall notify the Crick immediately. 6. The Data Recipient agrees to distribute a copy of these terms to the Authorised Personnel. The Data Recipient will procure that the Authorised Personnel comply with the terms of this agreement and will remain fully responsible for the Authorised Personnel’s non-compliance with this Agreement and/or applicable laws. Authorised Personnel must work under the direct supervision of the Principal Investigator of the Data Recipient (as set out in Section 1). 7. Should the Data Recipient wish to share these Data with an External Collaborator, the External Collaborator must complete and send to the Crick a separate application for access to these Data. 8. The Data Recipient 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, indirect, consequential, or incidental damages or losses arising from use of the Data), costs, awards damages and payments made by the Data Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Data 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. 9. The Data Recipient agrees to follow the Publication Policy in Section 4. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 10. Nothing in this Agreement shall operate to transfer to the Data Recipient any intellectual property rights to the Data. The Data Recipient 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. 11. The Data Recipient 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 Data Recipient agrees to implement licensing policies that will not obstruct further research and to follow the applicable laws of the Data Producer. 12. The Data Recipient agrees to destroy/discard the Data held, once it is no longer used for the Project, and at the latest 2 years after it is first accessed. 13. The Data Recipient will notify the Crick within 30 days of any changes or departures of Authorised Personnel. 14. The Data Recipient will notify the Crick prior to any significant changes to the protocol for the Project. 15. The Data Recipient will notify the Crick as soon as it becomes aware of a breach of the terms or conditions of this agreement. 16. The Crick may terminate this agreement by written notice to the Data Recipient. If this agreement terminates for any reason, the Data Recipient will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the Data Recipient from retaining these data for archival purpose in conformity with audit or legal requirements. 17. The Data Recipient accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than the Crick. In the event that changes are required, the Data Producers or their appointed agent will contact the Data Recipient to inform it of the changes and the Data Recipient may elect to accept the changes or terminate the agreement. 18. If requested, the Data Recipient will allow data security and management documentation to be inspected to verify that it is complying 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 England and Wales and shall be subject to the exclusive jurisdiction of the English courts. Section 3 File access: Data can be held in unencrypted files on an institutional computer system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. The Data Recipient shall store the Data only in the original encrypted form from EGA. The Data Recipient agrees and warrants that Data shall only be decrypted when necessary and only during the performance of the Project. At the end of the Project, the Data Recipient shall delete any decrypted files, including additional copies, any computer records or files containing Data that have been created by the Data Recipient’s automatic archiving and back-up procedures. The Data Recipient agrees and warrants that Data shall not be accessed: a) outside the Data Recipient’s network, including non-Data Recipient email systems; b) using unauthorized devices, including personal devices; c) via mobile and wireless devices, and devices on networks with wireless access points. Data shall not be stored on any portable device (laptop, smartphone, etc.) unless absolutely necessary and always strongly encrypted, and the portable devices shall always have password protected logins and screen locks, set to lock after maximum five (5) minutes of inactivity. Data written to removable storage media shall be automatically encrypted without the Data Recipient intervention. Section 4 – PUBLICATION POLICY 1. The Data Producers intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. The Data Producers anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. 2. The publication moratorium covers any Publications (including oral communications) that describe the use of the dataset and the Data Producers retain the right of first publication of its Data (or any part of the Data). The Data Recipient shall delay any Publication until the earlier of: (i) the Data Producers’ primary publication and (ii) twelve (12) months from the time the Data were deposited, unless the Data Producers have provided written consent to earlier submission for publication. The Data Recipient acknowledges that prompt publication or public disclosure of the results of the Research Project is encouraged and agrees that by publishing its global analyses of the Data, it will not disclose any results generated from the Data. 3. The Data Recipient may only publish Data if: (a) the Publication comprises only parts of the Data and not all of the Data; (b) it is not possible to establish the identity of any Research Participant from, or using, the Data contained in the publication; and (c) the publication complies with paragraph 4. 4. The Data Recipient shall ensure that each work based in whole or part on the Data that is authored by an Authorised Personnel acknowledges the published paper from which the Data derives, the version of the Data, and the role of the Crick source project and its funders in its distribution in accordance with customary scientific and academic practice. Further, the Data Recipient shall ensure that any Publication which contains, in any way, any patentable intellectual property shall be submitted to the Crick for review at least sixty (60) days prior to the intended publication. The Crick shall have thirty (30) days following receipt of the proposed Publication to review such publication and determine, if in the Crick’s reasonable opinion, a delay of the publication is necessary in order to protect its intellectual property (such delay not to exceed a period of six (6) months from the date of the Crick’s notice to the Data Recipient pursuant to this clause). 5. Further, within any permitted Publication including these Data the contribution of the Crick and the Data Producers shall be acknowledged in a manner consistent with the usual conventions in the field of research involved. 6. In any publications based on these Data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the Data Recipient with the Crick.

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
EGAS50000001791 Transcriptome Sequencing

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
EGAF00009007540 fastq.gz 400.2 MB
EGAF00009007544 fastq.gz 1.3 GB
EGAF00009007545 fastq.gz 171.4 MB
EGAF00009007547 fastq.gz 167.4 MB
EGAF00009007548 fastq.gz 401.4 MB
EGAF00009007549 fastq.gz 245.8 MB
EGAF00009007550 fastq.gz 890.3 MB
EGAF00009007551 fastq.gz 399.0 MB
EGAF00009007552 fastq.gz 245.8 MB
EGAF00009007557 fastq.gz 510.8 MB
EGAF00009007558 fastq.gz 519.4 MB
EGAF00009007559 fastq.gz 210.3 MB
EGAF00009007564 fastq.gz 190.4 MB
EGAF00009007567 fastq.gz 580.8 MB
EGAF00009007569 fastq.gz 193.6 MB
EGAF00009007570 fastq.gz 580.4 MB
EGAF00009007574 fastq.gz 592.9 MB
EGAF00009007575 fastq.gz 198.3 MB
EGAF00009007576 fastq.gz 593.7 MB
EGAF00009007580 fastq.gz 599.4 MB
EGAF00009007583 fastq.gz 163.7 MB
EGAF00009007590 fastq.gz 294.7 MB
EGAF00009007593 fastq.gz 506.4 MB
EGAF00009007594 fastq.gz 440.3 MB
EGAF00009007597 fastq.gz 870.8 MB
EGAF00009007598 fastq.gz 437.2 MB
EGAF00009007600 fastq.gz 295.5 MB
EGAF00009007601 fastq.gz 184.3 MB
EGAF00009007604 fastq.gz 187.8 MB
EGAF00009007609 fastq.gz 90.0 MB
EGAF00009007610 fastq.gz 194.4 MB
EGAF00009007616 fastq.gz 219.9 MB
EGAF00009007619 fastq.gz 454.0 MB
EGAF00009007622 fastq.gz 218.7 MB
EGAF00009007623 fastq.gz 1.2 GB
EGAF00009007624 fastq.gz 89.1 MB
EGAF00009007627 fastq.gz 219.3 MB
EGAF00009007631 fastq.gz 743.3 MB
EGAF00009007632 fastq.gz 153.2 MB
EGAF00009007633 fastq.gz 157.8 MB
EGAF00009007634 fastq.gz 155.1 MB
EGAF00009007637 fastq.gz 140.5 MB
EGAF00009007647 fastq.gz 345.0 MB
EGAF00009007654 fastq.gz 280.0 MB
EGAF00009007655 fastq.gz 290.3 MB
EGAF00009007659 fastq.gz 151.1 MB
EGAF00009007660 fastq.gz 279.5 MB
EGAF00009007661 fastq.gz 146.9 MB
EGAF00009007667 fastq.gz 152.1 MB
EGAF00009007676 fastq.gz 377.6 MB
EGAF00009007678 fastq.gz 331.6 MB
EGAF00009007679 fastq.gz 115.8 MB
EGAF00009007680 fastq.gz 149.0 MB
EGAF00009007681 fastq.gz 213.5 MB
EGAF00009007684 fastq.gz 66.3 MB
EGAF00009007685 fastq.gz 173.2 MB
EGAF00009007688 fastq.gz 169.3 MB
EGAF00009007689 fastq.gz 175.8 MB
EGAF00009007691 fastq.gz 168.4 MB
EGAF00009007699 fastq.gz 1.1 GB
EGAF00009007702 fastq.gz 1.4 GB
EGAF00009007703 fastq.gz 391.7 MB
EGAF00009007706 fastq.gz 1.6 GB
EGAF00009007712 fastq.gz 2.1 GB
EGAF00009007715 fastq.gz 2.2 GB
EGAF00009007716 fastq.gz 1.0 GB
EGAF00009007718 fastq.gz 1.8 GB
EGAF00009007720 fastq.gz 774.8 MB
EGAF00009007729 fastq.gz 716.9 MB
EGAF00009007730 fastq.gz 1.7 GB
EGAF00009007731 fastq.gz 171.5 MB
EGAF00009007732 fastq.gz 335.4 MB
EGAF00009007733 fastq.gz 217.1 MB
EGAF00009007734 fastq.gz 499.0 MB
EGAF00009007737 fastq.gz 498.3 MB
EGAF00009007741 fastq.gz 1.5 GB
EGAF00009007743 fastq.gz 1.6 GB
EGAF00009007746 fastq.gz 1.5 GB
EGAF00009007753 fastq.gz 1.8 GB
EGAF00009007757 fastq.gz 2.6 GB
EGAF00009007762 fastq.gz 395.1 MB
EGAF00009007766 fastq.gz 639.9 MB
EGAF00009007768 fastq.gz 2.3 GB
EGAF00009007770 fastq.gz 1.1 GB
EGAF00009007774 fastq.gz 652.3 MB
EGAF00009007776 fastq.gz 377.8 MB
EGAF00009007799 fastq.gz 85.8 MB
EGAF00009007801 fastq.gz 86.8 MB
EGAF00009007802 fastq.gz 2.2 GB
EGAF00009007811 fastq.gz 739.0 MB
EGAF00009007813 fastq.gz 2.5 GB
EGAF00009007814 fastq.gz 884.6 MB
EGAF00009007815 fastq.gz 759.7 MB
EGAF00009007816 fastq.gz 245.1 MB
EGAF00009007819 fastq.gz 598.7 MB
EGAF00009007820 fastq.gz 508.5 MB
EGAF00009007823 fastq.gz 227.1 MB
EGAF00009007824 fastq.gz 202.3 MB
EGAF00009007826 fastq.gz 136.0 MB
EGAF00009007827 fastq.gz 163.0 MB
EGAF00009007830 fastq.gz 87.8 MB
EGAF00009007833 fastq.gz 2.0 GB
EGAF00009007835 fastq.gz 357.4 MB
EGAF00009007839 fastq.gz 156.9 MB
EGAF00009007841 fastq.gz 222.0 MB
EGAF00009007844 fastq.gz 1.5 GB
EGAF00009007850 fastq.gz 1.7 GB
EGAF00009007856 fastq.gz 294.6 MB
EGAF00009007857 fastq.gz 909.9 MB
EGAF00009007860 fastq.gz 242.0 MB
EGAF00009007862 fastq.gz 212.9 MB
EGAF00009007864 fastq.gz 213.2 MB
EGAF00009007865 fastq.gz 213.7 MB
EGAF00009007866 fastq.gz 1.1 GB
EGAF00009007872 fastq.gz 201.8 MB
EGAF00009007874 fastq.gz 657.0 MB
EGAF00009007878 fastq.gz 160.7 MB
EGAF00009007881 fastq.gz 379.5 MB
EGAF00009007885 fastq.gz 163.8 MB
EGAF00009007889 fastq.gz 331.5 MB
EGAF00009007890 fastq.gz 437.5 MB
EGAF00009007891 fastq.gz 90.5 MB
EGAF00009007893 fastq.gz 359.4 MB
EGAF00009007895 fastq.gz 1.9 GB
EGAF00009007902 fastq.gz 283.0 MB
EGAF00009007904 fastq.gz 116.4 MB
EGAF00009007906 fastq.gz 1.5 GB
EGAF00009007913 fastq.gz 114.4 MB
EGAF00009007917 fastq.gz 88.2 MB
EGAF00009007920 fastq.gz 868.1 MB
EGAF00009007924 fastq.gz 1.0 GB
EGAF00009007931 fastq.gz 1.2 GB
EGAF00009007933 fastq.gz 169.9 MB
EGAF00009007935 fastq.gz 201.7 MB
EGAF00009007936 fastq.gz 1.2 GB
EGAF00009007945 fastq.gz 613.5 MB
EGAF00009007946 fastq.gz 181.9 MB
EGAF00009007950 fastq.gz 140.8 MB
EGAF00009007952 fastq.gz 88.7 MB
EGAF00009007954 fastq.gz 213.3 MB
EGAF00009007972 fastq.gz 2.1 GB
EGAF00009007979 fastq.gz 1.4 GB
EGAF00009007983 fastq.gz 195.2 MB
EGAF00009007986 fastq.gz 609.8 MB
EGAF00009007987 fastq.gz 187.0 MB
EGAF00009007991 fastq.gz 356.7 MB
EGAF00009007993 fastq.gz 371.3 MB
EGAF00009007994 fastq.gz 68.3 MB
EGAF00009007995 fastq.gz 66.8 MB
EGAF00009007999 fastq.gz 1.4 GB
EGAF00009008023 fastq.gz 2.5 GB
EGAF00009008053 fastq.gz 290.1 MB
EGAF00009008055 fastq.gz 1.3 GB
EGAF00009008057 fastq.gz 752.8 MB
EGAF00009008059 fastq.gz 519.3 MB
EGAF00009008061 fastq.gz 644.1 MB
EGAF00009008063 fastq.gz 508.0 MB
EGAF00009008065 fastq.gz 137.6 MB
EGAF00009008067 fastq.gz 113.0 MB
EGAF00009008068 fastq.gz 68.2 MB
160 Files (95.6 GB)