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Metagenomic characterization of tracheal aspirates from non-pulmonary sepsis patients

Metagenomic characterization of tracheal aspirates from non-pulmonary sepsis patients. This dataset consists of non-human read data from shotgun sequencing in sepsis case samples from lung aspirates. The dataset consist of 32 paired FASTQ files sequenced in paired-read mode 2x150 bp using an Illumina HiSeq 4000 sequencer.

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ITER-FIISC Data Access Committee (microbiome)

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. 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 Authorized 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 recognizing 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 analyzing 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 Organization 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 FIISC-ITER within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify FIISC-ITER. prior to any significant changes to the protocol for the Project. 14. The User Institution will notify FIISC-ITER as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. FIISC-ITER. 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 FIISC-ITER. 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 Authorized Personnel. The User Institution will procure that the Authorized Personnel comply with the terms of this agreement. 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 FIISC-ITER Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) - Dataset reference (EGA Study ID and Dataset Details) - Name of project that created the dataset - Names of other data producers/collaborators - Specific limitations on areas of research - Minimum protection measures required - File access: Data can be held in unencrypted files on an institutional compute 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. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (500 words max) All Individuals who the User Institution to be named as registered users +----------------------------------------------------------------------------+ | Name of Registered User | Email | Job Title | Supervisor* | +----------------------------------------------------------------------------+ All Individuals that should have an account created at the EGA +----------------------------------------------------------+ | Name of Registered User | Email | Job Title | +----------------------------------------------------------+ APPENDIX III – PUBLICATION POLICY FIISC-ITER 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. FIISC-ITER 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 6 months after these data were first made available on the relevant hosting database, unless FIISC-ITER. 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 (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 FIISC-ITER.

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
EGAS50000000384 Metagenomics

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
EGAF00008437350 fastq.gz 10.1 MB
EGAF00008437352 fastq.gz 9.8 MB
EGAF00008437354 fastq.gz 5.0 MB
EGAF00008437356 fastq.gz 5.3 MB
EGAF00008437357 fastq.gz 3.1 MB
EGAF00008437360 fastq.gz 3.2 MB
EGAF00008437361 fastq.gz 13.2 MB
EGAF00008437364 fastq.gz 12.6 MB
EGAF00008437366 fastq.gz 12.6 MB
EGAF00008437368 fastq.gz 11.6 MB
EGAF00008437369 fastq.gz 11.6 MB
EGAF00008437372 fastq.gz 11.0 MB
EGAF00008437374 fastq.gz 11.7 MB
EGAF00008437376 fastq.gz 11.2 MB
EGAF00008437378 fastq.gz 8.5 MB
EGAF00008437380 fastq.gz 8.1 MB
EGAF00008437382 fastq.gz 12.0 MB
EGAF00008437384 fastq.gz 11.1 MB
EGAF00008437386 fastq.gz 6.3 MB
EGAF00008437388 fastq.gz 5.8 MB
EGAF00008437391 fastq.gz 18.5 MB
EGAF00008437393 fastq.gz 276.5 MB
EGAF00008437394 fastq.gz 17.9 MB
EGAF00008437396 fastq.gz 291.3 MB
EGAF00008437397 fastq.gz 13.1 MB
EGAF00008437400 fastq.gz 13.0 MB
EGAF00008437401 fastq.gz 10.4 MB
EGAF00008437404 fastq.gz 10.1 MB
EGAF00008437407 fastq.gz 33.7 MB
EGAF00008437408 fastq.gz 9.0 MB
EGAF00008437411 fastq.gz 34.5 MB
EGAF00008437412 fastq.gz 8.1 MB
EGAF00008437414 fastq.gz 5.5 MB
EGAF00008437417 fastq.gz 5.7 MB
EGAF00008437418 fastq.gz 8.6 MB
EGAF00008437420 fastq.gz 9.1 MB
EGAF00008437429 fastq.gz 1.8 MB
EGAF00008437433 fastq.gz 1.9 MB
EGAF00008437435 fastq.gz 23.5 MB
EGAF00008437436 fastq.gz 24.3 MB
EGAF00008437437 fastq.gz 4.8 MB
EGAF00008437440 fastq.gz 5.0 MB
EGAF00008437441 fastq.gz 11.1 MB
EGAF00008437444 fastq.gz 11.4 MB
EGAF00008437446 fastq.gz 4.8 MB
EGAF00008437448 fastq.gz 5.1 MB
EGAF00008437451 fastq.gz 61.6 MB
EGAF00008437453 fastq.gz 64.5 MB
EGAF00008437455 fastq.gz 75.5 MB
EGAF00008437457 fastq.gz 81.1 MB
EGAF00008437459 fastq.gz 246.6 MB
EGAF00008437461 fastq.gz 30.8 MB
EGAF00008437463 fastq.gz 28.6 MB
EGAF00008437464 fastq.gz 315.5 MB
EGAF00008437466 fastq.gz 17.2 MB
EGAF00008437468 fastq.gz 17.4 MB
EGAF00008437469 fastq.gz 12.3 MB
EGAF00008437471 fastq.gz 12.6 MB
EGAF00008437474 fastq.gz 23.3 MB
EGAF00008437475 fastq.gz 25.7 MB
EGAF00008477585 fastq.gz 9.9 MB
EGAF00008477586 fastq.gz 10.6 MB
EGAF00008477587 fastq.gz 99.8 MB
EGAF00008477606 fastq.gz 92.3 MB
64 Files (2.3 GB)