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RNA sequencing and whole-genome mate-pair sequencing of osteosarcoma

This data set includes 72 mate pair sequenced osteosarcomas (36 as part of a discovery cohort and 36 as part of a validation cohort). It also includes RNA-sequencing data on 67 osteosarcomas (mostly overlapping with the above mate pair sequenced cases) and 13 osteoblastomas used as controls for gene expression levels.

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Data access policy for RNAseq and matepair data.

DATA ACCESS AGREEMENT between Lund University, P. O. Box 117, SE-221 00 Lund, Sweden, (hereinafter referred to as the “University”); and [name], [address], (hereinafter referred to as the “Recipient”); each a ‘Party’ and together the ‘Parties’. This agreement (the “Agreement”) is made on the last day of signature here below (the “Agreement Date”). BACKGROUND (A) The University’s Department of Laboratory Medicine, Division of Clinical Genetics is the owner of human genetic data relating to the research article by Saba et al. regarding genetic transposition of TP53 regulatory elements in osteosarcoma, for which the University has received approval from the Regional Ethics Committee (Regionala Etikprövningsnämnden) under the permission number Dnr 2011/289. (B) Pursuant to the request by the Recipient, the University has agreed to make the Data available to it for research purposes. OPERATIVE TERMS 1 Definitions and Interpretation 1.1 “User” means a researcher (or an individual conducting Research under the supervision of a researcher) who is employed by the Recipient and is bound by the terms and conditions of this Agreement. For the avoidance of doubt, “User” may also include students, visiting academics, contractors, sub-contractors or independent consultants provided that any such individual is bound by obligations no less onerous then those binding the Recipient’s employees. 1.2 ‘”Data” means the human genetic data obtained by the University. 1.3 “Data Subjects” means the individual to whom Data refers. 2 Access to Data 2.1 In consideration of the University agreeing to supply the Data to the Recipient, the Recipient agrees to be bound by the terms and conditions of this Agreement. The Recipient shall ensure that all Users are aware of and comply with the terms of the Agreement. 2.2 Recipient shall only use Data for the advancement of non-commercial biomedical research as specified in the data application form provided by the University and attached hereto as Appendix 1. 2.3 The Recipient agrees to only give access to Data, in whole or part, or any identifiable material derived from the Data, to Users. The Recipient agrees that before it gives any User access to Data, it shall first show the User a copy of this Agreement and shall inform the User that he or she must comply with the obligations contained in this Agreement and sign up to the provisions of this Agreement in the form set out at the end of this Agreement. The Recipient shall provide the University with a copy of the User’s acceptance form within thirty (30) days of the date of acceptance by the User. 2.4 The Recipient shall refer to the University all requests from third parties/persons not working under the direct supervision of the Recipient for supplies of the Data. 3 Data protection and confidentiality 3.1 Recipient agrees to comply with EU legislation on data protection when processing Data and to preserve, at all times, the confidentiality of the Data. Recipient further agrees to not attempt to identify the Data Subjects, redistribute the Data, or any subset or derivative of the Data, that could be used to identify the Data Subject, or in any other way compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy. 3.2 Where required under applicable laws regulating cross-border transfers of Personal Data, including European data protection laws, the parties, or their affiliates, will execute any further agreements or undertakings required to enable the lawful transfer of Personal Data, including where appropriate the EU standard contractual clauses for transfers of Personal Data to non-EU data processors set out in European Commission Decision 2010/87/EC of 5 February 2010 available at: http://eurlex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2010:039:0005:0018:EN:PDF or such standard contractual clauses as are then in force. 3.3 The Recipient agrees that it shall take all reasonable security precautions to keep the Data confidential, such precautions to be no less onerous than those applied in respect of the Recipient’s own confidential information. 4 Errors The Recipient agrees to notify the University of any errors detected in the Data. 5 Ownership of the Data 5.1 The Data and all intellectual property in them shall at all times remain the property of the University. 5.2 The Recipient and its Users shall have the right to develop Intellectual Property based on comparisons with their own data. Recipient and User recognise that nothing in this agreement shall operate to transfer to the Recipient any intellectual property rights relating to the Data. 6 Publications and reporting The Recipient agrees 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 University in its distribution. The Recipient will also declare in any such work that those who carried out the original analysis and collection of the Data bear no responsibility for the further analysis or interpretation of it by the Recipient. The Recipient undertakes that the Data and Confidential Information will only be used by the Recipient and Users for the sole purpose of the academic research and will not be used for any commercial purpose or commercially sponsored research. 7 Warranties 7.1 The Recipient accepts and agrees that the Data are experimental in nature and that they are supplied by the University on an ‘as is’ basis. The University makes no representation and gives no warranty or undertaking in relation to them whatsoever and excludes all implied warranties to the fullest extent permitted by law; 7.2 In particular, the University makes no representations or warranties, express or implied: • as to title, quality or fitness for a particular purpose or use of the Data; or • that the supply by the University or the use by the Recipient of the Data will not infringe the intellectual property rights of any third party. 7.3 The Recipient warrants that, in relation to the Data and their use: • they will comply with all relevant legislation and regulations; and • they have obtained all necessary consents and ethical approvals. 8 Liability 8.1 The University accepts no liability for loss of data, loss of profit, business or goodwill and all other indirect or consequential loss or damage suffered or incurred by the Recipient or by any other person arising from the supply of the Data or the use, keeping, or disposal of the Data. 8.2 The Recipient shall defend, indemnify and hold the University, its officers, employees and agents harmless against any loss, claim, damage or liability including reasonable legal costs and fees (of whatsoever kind or nature) which may arise in connection with the Recipient’s breach of this Agreement or the use, keeping, production or disposal of the Recipient or on its behalf, unless caused by the University’s gross negligence or wilful act or omission. 9 Termination 9.1 This Agreement shall take effect from the Agreement Date and will terminate on a Party giving 30 days’ prior written notice to the other; or upon breach by the Recipient or Users of any of the terms of this Agreement. 9.2 Upon termination of this Agreement or upon service of notice of termination by a Party for any reason whatsoever, the Recipient shall discontinue its use of the Data and shall, in accordance with the directions of the University, at its own cost and expense destroy the Data or return it to the University. 10 Notices 10.1 The Recipient will do all such acts and execute such documents as are required by the University to give effect to the terms of this Agreement or to enable the University to enjoy the full benefit of this Agreement (including but not limited to ownership of the Data and the arising intellectual property). 10.2 Recipient accepts that it may be necessary for the University 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 University or its appointed agent will contact Recipient to inform Recipient of any changes and Recipient agrees that Recipient’s continued use of the Data shall be dependent on the parties entering into a new version of the Agreement. 10.3 The Recipient may not assign or transfer all or any of its rights or obligations under this Agreement without the prior written consent of the University. 10.4 This Agreement is subject to Swedish substantive law. 10.5 Any dispute, controversy or claim arising out of or in connection with this Agreement, or the breach, termination or invalidity thereof, shall be solved by Swedish courts. This Agreement has been drawn up in two (2) original copies, each Party receiving one duly signed copy thereof. Signed …………………………….. Signed ……………………………… Authorised signature for and on behalf of Lund University Authorised signature for and on behalf of Recipient [please fill in the name of recipient] Name Name Position Position Dated Dated For the User (s):I acknowledge that I have read and understand the terms of this Agreement Signed ……………………………… Name Position Dated

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
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
EGAF00002558643 bam 12.4 GB
EGAF00002558644 bam 6.2 GB
EGAF00002558645 bam 6.4 GB
EGAF00002558646 bam 8.3 GB
EGAF00002558647 bam 13.8 GB
EGAF00002558648 bam 2.5 GB
EGAF00002558649 bam 11.4 GB
EGAF00002558650 bam 7.2 GB
EGAF00002558651 bam 7.6 GB
EGAF00002558652 bam 5.3 GB
EGAF00002558653 bam 8.7 GB
EGAF00002558654 bam 8.7 GB
EGAF00002558655 bam 9.6 GB
EGAF00002558656 bam 9.2 GB
EGAF00002558657 bam 8.1 GB
EGAF00002558658 bam 10.1 GB
EGAF00002558659 bam 10.0 GB
EGAF00002558660 bam 11.0 GB
EGAF00002558661 bam 5.1 GB
EGAF00002558662 bam 4.5 GB
EGAF00002558663 bam 9.0 GB
EGAF00002558664 bam 7.5 GB
EGAF00002558665 bam 8.5 GB
EGAF00002558666 bam 11.1 GB
EGAF00002558667 bam 9.5 GB
EGAF00002558668 bam 9.1 GB
EGAF00002558669 bam 3.7 GB
EGAF00002558670 bam 9.2 GB
EGAF00002558671 bam 8.3 GB
EGAF00002558672 bam 7.9 GB
EGAF00002558673 bam 9.0 GB
EGAF00002558674 bam 9.6 GB
EGAF00002558675 bam 8.8 GB
EGAF00002558676 bam 12.4 GB
EGAF00002558677 bam 11.1 GB
EGAF00002558678 bam 7.5 GB
EGAF00002558679 bam 7.3 GB
EGAF00002558680 bam 6.5 GB
EGAF00002558681 bam 6.2 GB
EGAF00002558682 bam 2.9 GB
EGAF00002558683 bam 8.2 GB
EGAF00002558684 bam 4.9 GB
EGAF00002558685 bam 5.7 GB
EGAF00002558686 bam 2.2 GB
EGAF00002558687 bam 10.4 GB
EGAF00002558688 bam 6.8 GB
EGAF00002558689 bam 10.8 GB
EGAF00002558690 bam 11.2 GB
EGAF00002558691 bam 6.2 GB
EGAF00002558692 bam 2.7 GB
EGAF00002558693 bam 1.9 GB
EGAF00002558694 bam 2.1 GB
EGAF00002558695 bam 1.6 GB
EGAF00002558696 bam 6.1 GB
EGAF00002558697 bam 8.4 GB
EGAF00002558698 bam 3.9 GB
EGAF00002558699 bam 1.4 GB
EGAF00002558700 bam 7.6 GB
EGAF00002558701 bam 8.0 GB
EGAF00002558702 bam 11.1 GB
EGAF00002558703 bam 7.5 GB
EGAF00002558704 bam 4.0 GB
EGAF00002558705 bam 1.5 GB
EGAF00002558706 bam 11.8 GB
EGAF00002558707 bam 6.7 GB
EGAF00002558708 bam 3.1 GB
EGAF00002558709 bam 7.1 GB
EGAF00002558710 bam 6.5 GB
EGAF00002558711 bam 7.3 GB
EGAF00002558712 bam 11.5 GB
EGAF00002558713 bam 7.8 GB
EGAF00002558714 bam 10.5 GB
EGAF00002558715 bam 8.0 GB
EGAF00002558716 bam 4.2 GB
EGAF00002558717 bam 7.4 GB
EGAF00002558718 bam 6.9 GB
EGAF00002558719 bam 4.4 GB
EGAF00002558720 bam 6.0 GB
EGAF00002558721 bam 7.4 GB
EGAF00002558722 bam 5.7 GB
EGAF00002558723 bam 7.1 GB
EGAF00002558724 bam 8.8 GB
EGAF00002558725 bam 8.0 GB
EGAF00002558726 bam 7.0 GB
EGAF00002558727 bam 8.6 GB
EGAF00002558728 bam 5.5 GB
EGAF00002558729 bam 5.5 GB
EGAF00002558730 bam 9.4 GB
EGAF00002558731 bam 6.3 GB
EGAF00002558732 bam 7.7 GB
EGAF00002558733 bam 7.3 GB
EGAF00002558734 bam 6.4 GB
EGAF00002558735 bam 9.5 GB
EGAF00002558736 bam 5.3 GB
EGAF00002558737 bam 8.2 GB
EGAF00002558738 bam 7.9 GB
EGAF00002558739 bam 5.3 GB
EGAF00002558740 bam 7.0 GB
EGAF00002558741 bam 4.7 GB
EGAF00002558742 bam 8.0 GB
EGAF00002558743 bam 7.4 GB
EGAF00002558744 bam 8.3 GB
EGAF00002558745 bam 7.9 GB
EGAF00002558746 bam 6.2 GB
EGAF00002558747 bam 7.7 GB
EGAF00002558748 bam 5.3 GB
EGAF00002558749 bam 6.0 GB
EGAF00002558750 bam 10.9 GB
EGAF00002558751 bam 5.7 GB
EGAF00002558752 bam 5.6 GB
EGAF00002558753 bam 6.4 GB
EGAF00002558754 bam 6.3 GB
EGAF00002558755 bam 6.1 GB
EGAF00002558756 bam 5.9 GB
EGAF00002558757 bam 5.5 GB
EGAF00002558758 bam 6.1 GB
EGAF00002558759 bam 6.6 GB
EGAF00002558760 bam 6.3 GB
EGAF00002558761 bam 7.2 GB
EGAF00002558762 bam 9.1 GB
EGAF00002558763 bam 5.0 GB
EGAF00002558764 bam 7.1 GB
EGAF00002558765 bam 8.0 GB
EGAF00002558766 bam 9.1 GB
EGAF00002558767 bam 7.1 GB
EGAF00002558768 bam 7.5 GB
EGAF00002558769 bam 5.1 GB
EGAF00002558770 bam 5.3 GB
EGAF00002558771 bam 6.6 GB
EGAF00002558772 bam 6.0 GB
EGAF00002558773 bam 6.9 GB
EGAF00002558774 bam 7.5 GB
EGAF00002558775 bam 7.7 GB
EGAF00002558776 bam 6.3 GB
EGAF00002558777 bam 6.1 GB
EGAF00002558778 bam 6.2 GB
EGAF00002558779 bam 7.4 GB
EGAF00002558780 bam 4.6 GB
EGAF00002558781 bam 6.2 GB
EGAF00002558782 bam 7.5 GB
EGAF00002558783 bam 5.9 GB
EGAF00002558784 bam 6.7 GB
EGAF00002558785 bam 6.9 GB
EGAF00002558786 bam 8.0 GB
EGAF00002558787 bam 7.3 GB
EGAF00002558788 bam 7.8 GB
EGAF00002558789 bam 7.1 GB
EGAF00002558790 bam 7.6 GB
EGAF00002558791 bam 7.6 GB
EGAF00002558792 bam 5.6 GB
EGAF00002558793 bam 5.8 GB
EGAF00002558794 bam 7.0 GB
EGAF00002558795 bam 7.1 GB
153 Files (1.1 TB)