RNA-seq of high grade serous ovarian tumours
Somatic RNA for 40 samples matched to the WGS was extracted using the Qiagen Qiasymphony RNA protcol (cat no 931636). The tissue was initially homogenised using a Qiagen Bioruptor, followed by the manufacturers recommended protocol (including DNase digestion). The resulting RNA the underwent quality control as follows: firstly, A260 and A280nm were measured on a Denovix DS-11 Fx to qualitatively illustrate A260/280nm and A260/230nm ratios as measures of RNA purity. A260/280 had to be 2.0 and A260/230 had to be 2.0-2.2. Then RNA was quantified using LifeTechnologies Qubit RNA BR kit (cat no Q10210). RNAseq was carried out by the Edinburgh Clinical Research Facility on an Illumina NExtSeq500. Total RNA samples were assessed on the Agilent Bioanalyser (Agilent Technologies, #G2939AA) with the RNA 6000 Nano Kit (#5067-1512) for quality and integrity of total RNA, and then quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, #Q32866) and the Qubit RNA HS assay kit (#Q32855). Libraries were prepared from total-RNA sample using the NEBNext Ultra 2 Directional RNA library prep kit for Illumina (#E7760S) with the NEBNext rRNA Depletion kit (#E6310) according to the provided protocol. 400ng of totalRNA was then added to the ribosomal RNA (rRNA) depletion reaction using the NEBNext rRNA depletion kit (Human/mouse/rat) (#E6310). This step uses specific probes that bind to the rRNA in order to cleave it. rRNA-depleted RNA was then DNase treated and purified using Agencourt RNAClean XP beads (Beckman Coulter Inc, #66514). RNA was then fragmented using random primers before undergoing first strand and second strand synthesis to create cDNA. cDNA was end repaired before ligation of sequencing adapters, and libraries were enriched by PCR using the NEBNext Multiplex oligos for Illumina set 1 and 2 (#E7500). Final libraries had an average peak size of 271bp. Libraries were quantified by fluorometry using the Qubit dsDNA HS assay and assessed for quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626). Sequencing was performed using the NextSeq 500/550 High-Output v2 (150 cycle) Kit (# FC- 404-2002) on the NextSeq 550 platform (Illumina Inc, #SY-415-1002). Libraries were combined in an equimolar pool based on the library quantification results and run across 5 High-Output Flow Cell v2.5.
- DAC: EGAC00001001588
- Technology: NextSeq 550
Data Access Agreement based on the EGA template, with modifications from University of Edinburgh. Please contact the data access committee for a copy of the form to request access.
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 “Data Access Agreement”). By signing this Agreement, the User Institution agrees to be bound by these terms and conditions. Definitions Agreement: means this Data Access Agreement. Authorised Personnel: The individuals at the User Institution to whom Provider Institution 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 and as set out in Appendix II. Data Producers: Provider Institution and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. EGA: The European Genome-phenome Archive. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. File Access Security: The minimum standard of file access security measures as set out in Appendix I 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 non-commercial 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. Provider Institution: The University Court of the University of Edinburgh, a charitable body registered in Scotland (registration number SC005336), incorporated under the Universities (Scotland) Acts and having its administrative offices located at Old College, South Bridge, Edinburgh, EH8 9YL. 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for the 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 comply with the File Access Security to protect these Data. 3. The User Institution agrees to undertake to protect the confidentiality of Research Participants in any research papers or publications that they prepare and/or publish by taking all best endeavours to ensure the identity of Research Participants is not disclosed. 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 and Data Access Agreement 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 of damages and payments made by the User Institution that may arise (whether directly or indirectly) in any way whatsoever from the User Institution’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 (https://www.genome.gov/Pages/Research/WellcomeReport0303.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 comply with the Publication Policy as set out in 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 delete the Data transferred from the Data Producers, once it is no longer required to be used for the Project or after the agreed data retention period has expired (whichever comes first), unless obliged to retain the data for archival purposes in conformity with audit or legal requirements and all in accordance with the File Access Security 12. The User Institution will notify Provider Institution within 30 days of any changes or departures of any Authorised Personnel. 13. The User Institution will notify Provider Institution prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Provider Institution as soon as it becomes aware of a breach of the terms or conditions of this Agreement. 15. Provider Institution 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. As an example, this may include specific provisions relating to the Data required by Data Producers other than Provider Institution. 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 hereby procures that the Authorised Personnel shall 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 Scotland and shall be subject to the exclusive jurisdiction of the Scottish courts. Agreed for and on behalf of the User Institution Name of User Institution: Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for and on behalf of the Provider Institution Signature: Name: Title: Date: DATA ACCESS AGREEMENT APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) Whole genome sequencing data of tumour/normal matched pairs for 110 patients with high grade serous ovarian carcinoma in FASTQ format. Name of project that created the dataset Astra Zeneca-Stratified Medicine Scotland partnership – Ovarian cancer stratification Names of other Data Producers/collaborators The paired samples were provided by NHS Lothian, NHS Greater Glasgow and Clyde, NHS Tayside and NHS Grampian. Other collaborators were The University of Glasgow, The University of Dundee and the University of Aberdeen. Specific limitations on areas of research N/A Minimum protection measures required File Access Security: Only Authorised Personnel may have access to both the raw and any associated downstream processed filesets for the duration of the Project and these should not be shared with non-Authorised Personnel (see Appendix II). The Data shall be held in unencrypted files on a secure institutional computer system requiring user log in, 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 shall 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 and only stored for the minimum length of time required (i.e. for data transfer). The raw datasets provided should be deleted from all file systems no longer than 12 months after the approval has been granted under the terms of this Data Access Agreement. This time period does not apply to any downstream processed data files which can be kept for the duration of the project. The Data shall at all times be used in accordance with the terms of EGA policy on the Implementation of the EU General Data Protection Regulation (GDPR) as set out at: https://ega-archive.org/privacy-notice DATA ACCESS AGREEMENT APPENDIX II – PROJECT DETAILS Name of User Institution: (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number (to be completed by the Requestor) Brief abstract of the Project in which the Data will be used (500 words max) (to be completed by the Requestor) All individuals who the User Institution seeks to be named as registered users Name of Registered User Email Job Title Supervisor (to be completed by the Requester) All individuals that should have an account created at the EGA Name of Registered User Email Job Title (to be completed by the Requester) DATA ACCESS AGREEMENT APPENDIX III – PUBLICATION POLICY The Provider Institution intends 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 Provider Institution anticipates 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. The publication moratorium covers any publications (including oral communications) that describe the use of the Data. The User Institution agrees to follow the publication criteria set out below: • For research papers, submission for publication should not occur until 6 months after these Data were first made available on the relevant hosting database, unless Provider Institution has provided written consent to agree to an earlier submission. • In any publications result on the Data provided here, the Data sets must be correctly referenced , 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 User Institution with Provider Institution. • Any publication must cite the following acknowledgement: ‘This publication would not have been possible without the support of the Institute of Genetics and Cancer at the University of Edinburgh, the Nicola Murray Centre for Ovarian Cancer Research and the Astra Zeneca-Stratified Medicine Scotland partnership’ • Prior to publication, the User Institution shall check with the Data Producers to ensure that the most relevant publications, with respect to the Data, are cited in their work.
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 | |
|---|---|---|---|---|
| EGAF00004169600 | fastq.gz | 2.6 GB | ||
| EGAF00004169601 | fastq.gz | 2.6 GB | ||
| EGAF00004169602 | fastq.gz | 3.2 GB | ||
| EGAF00004169603 | fastq.gz | 3.3 GB | ||
| EGAF00004169604 | fastq.gz | 3.4 GB | ||
| EGAF00004169605 | fastq.gz | 3.5 GB | ||
| EGAF00004169606 | fastq.gz | 2.6 GB | ||
| EGAF00004169607 | fastq.gz | 2.7 GB | ||
| EGAF00004169610 | fastq.gz | 2.7 GB | ||
| EGAF00004169611 | fastq.gz | 2.7 GB | ||
| EGAF00004169612 | fastq.gz | 2.5 GB | ||
| EGAF00004169613 | fastq.gz | 2.5 GB | ||
| EGAF00004169614 | fastq.gz | 2.7 GB | ||
| EGAF00004169615 | fastq.gz | 2.8 GB | ||
| EGAF00004169616 | fastq.gz | 2.8 GB | ||
| EGAF00004169617 | fastq.gz | 2.8 GB | ||
| EGAF00004169618 | fastq.gz | 2.7 GB | ||
| EGAF00004169619 | fastq.gz | 2.8 GB | ||
| EGAF00004169620 | fastq.gz | 2.6 GB | ||
| EGAF00004169621 | fastq.gz | 2.7 GB | ||
| EGAF00004169622 | fastq.gz | 2.4 GB | ||
| EGAF00004169623 | fastq.gz | 2.5 GB | ||
| EGAF00004169624 | fastq.gz | 2.3 GB | ||
| EGAF00004169625 | fastq.gz | 2.4 GB | ||
| EGAF00004169626 | fastq.gz | 2.2 GB | ||
| EGAF00004169627 | fastq.gz | 2.2 GB | ||
| EGAF00004169628 | fastq.gz | 3.4 GB | ||
| EGAF00004169629 | fastq.gz | 3.5 GB | ||
| EGAF00004169630 | fastq.gz | 2.7 GB | ||
| EGAF00004169631 | fastq.gz | 2.8 GB | ||
| EGAF00004169632 | fastq.gz | 2.9 GB | ||
| EGAF00004169633 | fastq.gz | 2.9 GB | ||
| EGAF00004169636 | fastq.gz | 2.8 GB | ||
| EGAF00004169637 | fastq.gz | 2.8 GB | ||
| EGAF00004169638 | fastq.gz | 2.6 GB | ||
| EGAF00004169639 | fastq.gz | 2.6 GB | ||
| EGAF00004169640 | fastq.gz | 2.1 GB | ||
| EGAF00004169641 | fastq.gz | 2.2 GB | ||
| EGAF00004169642 | fastq.gz | 2.3 GB | ||
| EGAF00004169643 | fastq.gz | 2.5 GB | ||
| EGAF00004169644 | fastq.gz | 2.3 GB | ||
| EGAF00004169645 | fastq.gz | 2.4 GB | ||
| EGAF00004169646 | fastq.gz | 2.3 GB | ||
| EGAF00004169647 | fastq.gz | 2.3 GB | ||
| EGAF00004169648 | fastq.gz | 3.0 GB | ||
| EGAF00004169649 | fastq.gz | 3.1 GB | ||
| EGAF00004169650 | fastq.gz | 3.6 GB | ||
| EGAF00004169651 | fastq.gz | 3.7 GB | ||
| EGAF00004169652 | fastq.gz | 6.0 GB | ||
| EGAF00004169653 | fastq.gz | 6.1 GB | ||
| EGAF00004169654 | fastq.gz | 2.1 GB | ||
| EGAF00004169655 | fastq.gz | 2.1 GB | ||
| EGAF00004169656 | fastq.gz | 2.2 GB | ||
| EGAF00004169657 | fastq.gz | 2.3 GB | ||
| EGAF00004169658 | fastq.gz | 2.5 GB | ||
| EGAF00004169659 | fastq.gz | 2.5 GB | ||
| EGAF00004169660 | fastq.gz | 3.3 GB | ||
| EGAF00004169661 | fastq.gz | 3.4 GB | ||
| EGAF00004169662 | fastq.gz | 2.4 GB | ||
| EGAF00004169663 | fastq.gz | 2.5 GB | ||
| EGAF00004169664 | fastq.gz | 2.8 GB | ||
| EGAF00004169665 | fastq.gz | 2.9 GB | ||
| EGAF00004169666 | fastq.gz | 3.0 GB | ||
| EGAF00004169667 | fastq.gz | 3.0 GB | ||
| EGAF00004169668 | fastq.gz | 3.3 GB | ||
| EGAF00004169669 | fastq.gz | 3.4 GB | ||
| EGAF00004169670 | fastq.gz | 2.2 GB | ||
| EGAF00004169671 | fastq.gz | 2.3 GB | ||
| EGAF00004169672 | fastq.gz | 2.3 GB | ||
| EGAF00004169673 | fastq.gz | 2.3 GB | ||
| EGAF00004169674 | fastq.gz | 2.5 GB | ||
| EGAF00004169675 | fastq.gz | 2.6 GB | ||
| EGAF00004169676 | fastq.gz | 2.3 GB | ||
| EGAF00004169677 | fastq.gz | 2.3 GB | ||
| EGAF00004169678 | fastq.gz | 2.7 GB | ||
| EGAF00004169679 | fastq.gz | 2.7 GB | ||
| EGAF00004169680 | fastq.gz | 3.1 GB | ||
| EGAF00004169681 | fastq.gz | 3.2 GB | ||
| EGAF00004169682 | fastq.gz | 3.6 GB | ||
| EGAF00004169683 | fastq.gz | 3.7 GB | ||
| 80 Files (224.6 GB) | ||||