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ST dataset from subcortical white matter MS lesions (CA & CI) and controls

This dataset contains the FASTQ files, the correspondent H&E pictures with the fiducial frames and the json files that were used for the spatial transcriptomic analysis in our paper (n=19). Within the json files names, one can find the information about the slide name (V11M111-111) and the capture area (A1) for each sample.

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DAC SubcorticalMS_ST_snRNAseq Data Access Policy

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 Authorized Personnel: The individuals at the User Institution to whom the DAC SubcorticalMS_ST_snRNAseq 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 Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The DAC SubcorticalMS_ST_snRNAseq 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. DAC SubcorticalMS_ST_snRNAseq: Data Access Committee, Laboratory of Lucas Schirmer, Medical Faculty Mannheim, Heidelberg University, Germany 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 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 the DAC SubcorticalMS_ST_snRNAseq within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify the DAC SubcorticalMS_ST_snRNAseq prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the DAC SubcorticalMS_ST_snRNAseq as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The DAC SubcorticalMS_ST_snRNAseq 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 the DAC SubcorticalMS_ST_snRNAseq. 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.

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
EGAS50000000353 RNASeq
  • Changed title
  • Added information
  • Dataset Released

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
EGAF50000110435 fastq.gz 17.1 GB
EGAF50000110436 fastq.gz 21.0 GB
EGAF50000110437 fastq.gz 2.5 GB
EGAF50000110438 fastq.gz 2.3 GB
EGAF50000110439 fastq.gz 10.7 GB
EGAF50000110440 fastq.gz 1.5 GB
EGAF50000110441 fastq.gz 12.2 GB
EGAF50000110442 fastq.gz 1.5 GB
EGAF50000110443 fastq.gz 5.7 GB
EGAF50000110444 fastq.gz 6.3 GB
EGAF50000110445 fastq.gz 784.8 MB
EGAF50000110446 fastq.gz 741.5 MB
EGAF50000110447 fastq.gz 4.4 GB
EGAF50000110448 fastq.gz 635.9 MB
EGAF50000110449 fastq.gz 5.3 GB
EGAF50000110450 fastq.gz 640.0 MB
EGAF50000110451 fastq.gz 11.1 GB
EGAF50000110452 fastq.gz 1.5 GB
EGAF50000110453 fastq.gz 12.8 GB
EGAF50000110454 fastq.gz 1.5 GB
EGAF50000110455 fastq.gz 5.9 GB
EGAF50000110456 fastq.gz 4.9 GB
EGAF50000110457 fastq.gz 765.2 MB
EGAF50000110458 fastq.gz 671.9 MB
EGAF50000110459 fastq.gz 5.9 GB
EGAF50000110460 fastq.gz 833.2 MB
EGAF50000110461 fastq.gz 851.7 MB
EGAF50000110462 fastq.gz 6.9 GB
EGAF50000110463 fastq.gz 5.3 GB
EGAF50000110464 fastq.gz 782.1 MB
EGAF50000110465 fastq.gz 6.1 GB
EGAF50000110466 fastq.gz 782.0 MB
EGAF50000110467 fastq.gz 11.1 GB
EGAF50000110468 fastq.gz 1.4 GB
EGAF50000110469 fastq.gz 9.9 GB
EGAF50000110470 fastq.gz 1.3 GB
EGAF50000110471 fastq.gz 13.0 GB
EGAF50000110472 fastq.gz 1.6 GB
EGAF50000110473 fastq.gz 13.8 GB
EGAF50000110474 fastq.gz 1.7 GB
EGAF50000110475 fastq.gz 5.2 GB
EGAF50000110476 fastq.gz 743.9 MB
EGAF50000110477 fastq.gz 5.8 GB
EGAF50000110478 fastq.gz 721.7 MB
EGAF50000110479 fastq.gz 5.9 GB
EGAF50000110480 fastq.gz 854.3 MB
EGAF50000110481 fastq.gz 993.4 MB
EGAF50000110482 fastq.gz 7.0 GB
EGAF50000110483 fastq.gz 1.3 GB
EGAF50000110484 fastq.gz 11.6 GB
EGAF50000110485 fastq.gz 1.4 GB
EGAF50000110486 fastq.gz 9.9 GB
EGAF50000110487 fastq.gz 5.5 GB
EGAF50000110488 fastq.gz 845.0 MB
EGAF50000110489 fastq.gz 6.6 GB
EGAF50000110490 fastq.gz 792.8 MB
EGAF50000110491 fastq.gz 9.6 GB
EGAF50000110492 fastq.gz 1.3 GB
EGAF50000110493 fastq.gz 1.3 GB
EGAF50000110494 fastq.gz 11.0 GB
EGAF50000110495 fastq.gz 1.1 GB
EGAF50000110496 fastq.gz 8.1 GB
EGAF50000110497 fastq.gz 1.1 GB
EGAF50000110498 fastq.gz 9.1 GB
EGAF50000110499 fastq.gz 1.2 GB
EGAF50000110500 fastq.gz 1.2 GB
EGAF50000110501 fastq.gz 14.0 GB
EGAF50000110502 fastq.gz 14.4 GB
EGAF50000110513 fastq.gz 2.6 GB
EGAF50000110514 fastq.gz 32.7 GB
EGAF50000110515 fastq.gz 34.1 GB
EGAF50000110516 fastq.gz 2.6 GB
EGAF50000110561 json 569.5 kB
EGAF50000110562 tif 124.9 MB
EGAF50000110563 tif 127.1 MB
EGAF50000110564 json 570.0 kB
EGAF50000110565 json 567.5 kB
EGAF50000110566 tif 117.2 MB
EGAF50000110567 json 558.2 kB
EGAF50000110568 tif 120.0 MB
EGAF50000110569 json 577.3 kB
EGAF50000110570 tif 124.8 MB
EGAF50000110571 json 550.4 kB
EGAF50000110572 tif 158.4 MB
EGAF50000110573 json 565.6 kB
EGAF50000110574 tif 119.1 MB
EGAF50000110575 json 567.2 kB
EGAF50000110576 tif 133.6 MB
EGAF50000110577 json 570.8 kB
EGAF50000110578 tif 122.8 MB
EGAF50000110579 json 564.3 kB
EGAF50000110580 tif 122.8 MB
EGAF50000110581 json 569.7 kB
EGAF50000110582 tif 122.0 MB
EGAF50000110583 json 557.8 kB
EGAF50000110584 tif 506.6 MB
EGAF50000110585 json 547.9 kB
EGAF50000110586 tif 124.9 MB
EGAF50000110588 json 570.6 kB
EGAF50000110589 tif 497.5 MB
EGAF50000110590 json 570.9 kB
EGAF50000110591 tif 120.3 MB
EGAF50000110592 json 567.7 kB
EGAF50000110593 tif 123.3 MB
EGAF50000110594 json 573.7 kB
EGAF50000110595 tif 514.6 MB
EGAF50000110603 json 547.2 kB
EGAF50000110604 tif 512.8 MB
108 Files (427.9 GB)