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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16S V3-V4 sequencing of lung microbiota from 17 NSCLC patients eligible for surgery without neoadjuvant treatment

This dataset is composed of 86 samples: 15 samples of bronchoalveolar lavage fluid (BAL), 17 samples of non-malignant lung tissue, 14 samples of peritumoural tissue, 16 tumour tissues, 8 negative DNA extraction controls, 16 negative sampling controls for BAL. Samples were obtained from 17 NSCLC patients (average age 68 years). Sequenced region was 16S V3-V4. Fastq files are provided.

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DAA - MICA Pchir lung microbiota

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 User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom Centre Jean Perrin 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. Data Producers: Centre Jean Perrin and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. 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 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. Centre Jean Perrin: Comprehensive Cancer Center; 58 rue Montalembert, 63011 Clermont Ferrand, France 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for 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 use at least the measures set out in Appendix I to protect these Data. 3. The User Institution 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 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 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 damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the 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. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.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 follow the Publication Policy 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 destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify Centre Jean Perrin within 30 days of any changes or departures of Authorised Personnel. Data stored on this person’s computer or laptop, as well as back-up copies of the data are to be destroyed. 13. The User Institution will notify Centre Jean Perrin prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Centre Jean Perrin as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Centre Jean Perrin 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 Centre Jean Perrin. 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 will procure that the Authorised Personnel 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 England and Wales and shall be subject to the exclusive jurisdiction of the English courts. Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for Centre Jean Perrin Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY   APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details): EGA Study ID: EGAS00001004728 Dataset Details: Name of project that created the dataset: MICA Trial (NCT03068663): Characterization of Microbiota (Intestinal, From Lungs, and Upper Airways) in Patients With Non-small Cell Lung Carcinoma: Exploratory Study Names of other data producers/collaborators: Centre Jean Perrin Specific limitations on areas of research: Data access is limited to scientific community only for the purpose of scientific review, control and validation of the results reported in the adjacent publications (as noted in the patients’ informed consent). Data should not be sent outside the European Union. Data access: Access will be granted to User Institution for 4 months, during which the Authorised Personnel is free to access and download referenced dataset. At the end of the 4 months, the access will be suspended. Minimum protection measures required: Unencrypted data can be held only on personalized institutional laptops or computers protected with unique passphrase known only to Authorised User and with screen locks (set to lock after 5 min of inactivity max). Laptops and computers must be equipped with up-to-date and active antivirus system and firewall. They can have Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. If stored on internal institutional servers or any type of portable hard drives, data must be encrypted. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number The requested dataset will be used for (please choose the appropriate): ☐ Scientific review (peer-review) ☐ Data control ☐ Validation of results Brief abstract of the Project in which the Data will be used (500 words max) All Individuals of the User Institution to be named as registered users Name of Registered User Email^ Job Title Supervisor* ^only institutional email address will be considered All Individuals that should have an account created at the EGA Name of Registered User Email Job Title   APPENDIX III – PUBLICATION POLICY Centre Jean Perrin 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. Centre Jean Perrin 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. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until 56 months after these data were first made available on the relevant hosting database, unless Centre Jean Perrin has provided written consent to earlier submission. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (i.e. 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 Centre Jean Perrin.

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
EGAS00001004728 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
EGAF00004835660 fastq.gz 5.2 MB Report
EGAF00004835661 fastq.gz 6.3 MB Report
EGAF00004835662 fastq.gz 3.7 MB Report
EGAF00004835663 fastq.gz 3.8 MB Report
EGAF00004835664 fastq.gz 6.2 MB Report
EGAF00004835665 fastq.gz 7.2 MB Report
EGAF00004835666 fastq.gz 3.4 MB Report
EGAF00004835667 fastq.gz 3.8 MB Report
EGAF00004835668 fastq.gz 7.5 MB Report
EGAF00004835669 fastq.gz 7.9 MB Report
EGAF00004835670 fastq.gz 7.2 MB Report
EGAF00004835671 fastq.gz 8.7 MB Report
EGAF00004835672 fastq.gz 5.4 MB Report
EGAF00004835673 fastq.gz 6.2 MB Report
EGAF00004835674 fastq.gz 4.1 MB Report
EGAF00004835675 fastq.gz 4.8 MB Report
EGAF00004835676 fastq.gz 5.5 MB Report
EGAF00004835677 fastq.gz 6.4 MB Report
EGAF00004835678 fastq.gz 5.5 MB Report
EGAF00004835679 fastq.gz 6.7 MB Report
EGAF00004835680 fastq.gz 6.3 MB Report
EGAF00004835681 fastq.gz 7.0 MB Report
EGAF00004835682 fastq.gz 3.7 MB Report
EGAF00004835683 fastq.gz 4.6 MB Report
EGAF00004835684 fastq.gz 11.7 MB Report
EGAF00004835685 fastq.gz 15.2 MB Report
EGAF00004835686 fastq.gz 5.5 MB Report
EGAF00004835687 fastq.gz 7.1 MB Report
EGAF00004835688 fastq.gz 4.8 MB Report
EGAF00004835689 fastq.gz 6.8 MB Report
EGAF00004835690 fastq.gz 50.9 MB Report
EGAF00004835691 fastq.gz 63.5 MB Report
EGAF00004835692 fastq.gz 8.6 MB Report
EGAF00004835693 fastq.gz 10.4 MB Report
EGAF00004835694 fastq.gz 9.8 MB Report
EGAF00004835695 fastq.gz 12.1 MB Report
EGAF00004835696 fastq.gz 6.7 MB Report
EGAF00004835697 fastq.gz 8.4 MB Report
EGAF00004835698 fastq.gz 4.4 MB Report
EGAF00004835699 fastq.gz 5.1 MB Report
EGAF00004835700 fastq.gz 2.9 MB Report
EGAF00004835701 fastq.gz 3.2 MB Report
EGAF00004835702 fastq.gz 3.2 MB Report
EGAF00004835703 fastq.gz 3.9 MB Report
EGAF00004835704 fastq.gz 12.3 MB Report
EGAF00004835705 fastq.gz 14.5 MB Report
EGAF00004835706 fastq.gz 3.7 MB Report
EGAF00004835707 fastq.gz 3.8 MB Report
EGAF00004835708 fastq.gz 4.1 MB Report
EGAF00004835709 fastq.gz 4.5 MB Report
EGAF00004835710 fastq.gz 4.3 MB Report
EGAF00004835711 fastq.gz 4.6 MB Report
EGAF00004835712 fastq.gz 6.0 MB Report
EGAF00004835713 fastq.gz 6.7 MB Report
EGAF00004835714 fastq.gz 7.0 MB Report
EGAF00004835715 fastq.gz 8.0 MB Report
EGAF00004835716 fastq.gz 6.0 MB Report
EGAF00004835717 fastq.gz 7.5 MB Report
EGAF00004835718 fastq.gz 7.1 MB Report
EGAF00004835719 fastq.gz 7.5 MB Report
EGAF00004835720 fastq.gz 7.0 MB Report
EGAF00004835721 fastq.gz 7.4 MB Report
EGAF00004835722 fastq.gz 7.1 MB Report
EGAF00004835723 fastq.gz 8.4 MB Report
EGAF00004835724 fastq.gz 8.2 MB Report
EGAF00004835725 fastq.gz 9.4 MB Report
EGAF00004835726 fastq.gz 5.0 MB Report
EGAF00004835727 fastq.gz 5.7 MB Report
EGAF00004835728 fastq.gz 9.4 MB Report
EGAF00004835729 fastq.gz 10.8 MB Report
EGAF00004835730 fastq.gz 4.6 MB Report
EGAF00004835731 fastq.gz 5.2 MB Report
EGAF00004835732 fastq.gz 3.7 MB Report
EGAF00004835733 fastq.gz 3.8 MB Report
EGAF00004835734 fastq.gz 3.3 MB Report
EGAF00004835735 fastq.gz 3.6 MB Report
EGAF00004835736 fastq.gz 6.3 MB Report
EGAF00004835737 fastq.gz 7.2 MB Report
EGAF00004835738 fastq.gz 6.4 MB Report
EGAF00004835739 fastq.gz 7.1 MB Report
EGAF00004835740 fastq.gz 6.7 MB Report
EGAF00004835741 fastq.gz 7.2 MB Report
EGAF00004835742 fastq.gz 4.1 MB Report
EGAF00004835743 fastq.gz 4.5 MB Report
EGAF00004835744 fastq.gz 9.0 MB Report
EGAF00004835745 fastq.gz 10.7 MB Report
EGAF00004835746 fastq.gz 5.6 MB Report
EGAF00004835747 fastq.gz 5.9 MB Report
EGAF00004835748 fastq.gz 4.7 MB Report
EGAF00004835749 fastq.gz 4.8 MB Report
EGAF00004835750 fastq.gz 4.8 MB Report
EGAF00004835751 fastq.gz 5.2 MB Report
EGAF00004835752 fastq.gz 4.5 MB Report
EGAF00004835753 fastq.gz 5.2 MB Report
EGAF00004835754 fastq.gz 4.7 MB Report
EGAF00004835755 fastq.gz 4.9 MB Report
EGAF00004835756 fastq.gz 3.5 MB Report
EGAF00004835757 fastq.gz 4.1 MB Report
EGAF00004835758 fastq.gz 7.0 MB Report
EGAF00004835759 fastq.gz 8.2 MB Report
EGAF00004835760 fastq.gz 4.4 MB Report
EGAF00004835761 fastq.gz 5.2 MB Report
EGAF00004835762 fastq.gz 3.4 MB Report
EGAF00004835763 fastq.gz 3.6 MB Report
EGAF00004835764 fastq.gz 7.0 MB Report
EGAF00004835765 fastq.gz 8.2 MB Report
EGAF00004835766 fastq.gz 10.4 MB Report
EGAF00004835767 fastq.gz 12.2 MB Report
EGAF00004835768 fastq.gz 5.3 MB Report
EGAF00004835769 fastq.gz 6.5 MB Report
EGAF00004835770 fastq.gz 2.9 MB Report
EGAF00004835771 fastq.gz 3.4 MB Report
EGAF00004835772 fastq.gz 4.4 MB Report
EGAF00004835773 fastq.gz 4.9 MB Report
EGAF00004835774 fastq.gz 6.5 MB Report
EGAF00004835775 fastq.gz 7.7 MB Report
EGAF00004835776 fastq.gz 4.3 MB Report
EGAF00004835777 fastq.gz 5.2 MB Report
EGAF00004835778 fastq.gz 11.1 MB Report
EGAF00004835779 fastq.gz 13.5 MB Report
EGAF00004835780 fastq.gz 9.3 MB Report
EGAF00004835781 fastq.gz 10.7 MB Report
EGAF00004835782 fastq.gz 7.8 MB Report
EGAF00004835783 fastq.gz 8.4 MB Report
EGAF00004835784 fastq.gz 13.0 kB Report
EGAF00004835785 fastq.gz 14.6 kB Report
EGAF00004835786 fastq.gz 6.1 kB Report
EGAF00004835787 fastq.gz 6.8 kB Report
EGAF00004835788 fastq.gz 8.1 kB Report
EGAF00004835789 fastq.gz 9.8 kB Report
EGAF00004835790 fastq.gz 8.7 kB Report
EGAF00004835791 fastq.gz 9.7 kB Report
EGAF00004835792 fastq.gz 8.2 kB Report
EGAF00004835793 fastq.gz 9.3 kB Report
EGAF00004835794 fastq.gz 9.4 kB Report
EGAF00004835795 fastq.gz 10.3 kB Report
EGAF00004835796 fastq.gz 9.6 kB Report
EGAF00004835797 fastq.gz 10.1 kB Report
EGAF00004835798 fastq.gz 10.3 kB Report
EGAF00004835799 fastq.gz 11.2 kB Report
EGAF00004835800 fastq.gz 49.0 kB Report
EGAF00004835801 fastq.gz 54.3 kB Report
EGAF00004835802 fastq.gz 45.6 kB Report
EGAF00004835803 fastq.gz 52.2 kB Report
EGAF00004835804 fastq.gz 34.2 kB Report
EGAF00004835805 fastq.gz 38.5 kB Report
EGAF00004835806 fastq.gz 50.3 kB Report
EGAF00004835807 fastq.gz 55.2 kB Report
EGAF00004835808 fastq.gz 72.2 kB Report
EGAF00004835809 fastq.gz 83.2 kB Report
EGAF00004835810 fastq.gz 18.8 kB Report
EGAF00004835811 fastq.gz 19.8 kB Report
EGAF00004835812 fastq.gz 28.8 kB Report
EGAF00004835813 fastq.gz 29.9 kB Report
EGAF00004835814 fastq.gz 19.6 kB Report
EGAF00004835815 fastq.gz 22.6 kB Report
EGAF00004835816 fastq.gz 7.8 kB Report
EGAF00004835817 fastq.gz 8.8 kB Report
EGAF00004835818 fastq.gz 8.7 kB Report
EGAF00004835819 fastq.gz 9.9 kB Report
EGAF00004835820 fastq.gz 30.7 kB Report
EGAF00004835821 fastq.gz 34.2 kB Report
EGAF00004835822 fastq.gz 11.6 kB Report
EGAF00004835823 fastq.gz 12.1 kB Report
EGAF00004835824 fastq.gz 21.7 kB Report
EGAF00004835825 fastq.gz 24.0 kB Report
EGAF00004835826 fastq.gz 15.8 kB Report
EGAF00004835827 fastq.gz 17.6 kB Report
EGAF00004835828 fastq.gz 126.5 kB Report
EGAF00004835829 fastq.gz 149.3 kB Report
EGAF00004835830 fastq.gz 62.0 kB Report
EGAF00004835831 fastq.gz 72.2 kB Report
172 Files (901.9 MB)