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Single-cell RNA and TCR sequencing FASTQ files for EBV-specific CD8+ T cells in 21 Multiple Sclerosis and 19 control participants

This dataset includes paired gene expression (GEX), cell surface protein (CSP) and T cell receptor (VDJ) FASTQ files obtained from 21 MS and 19 control participants. Briefly, cryopreserved PBMCs were thawed and stained with DNA-barcoded dCODE-dextamers to identify EBV antigen-specific T cells, together with sample hashtag antibodies compatible with the 10x Genomics 5′ Feature Barcode workflow. Details for hashtag antibodies and multiplex format is available in the manuscript. Following staining, samples were processed using the Chromium GEM-X Single Cell 5′ Gene Expression and V(D)J workflow with Feature Barcode technology, according to the manufacturer’s instructions. Amplified cDNA was used to generate separate 5′ GEX, CSP and VDJ libraries. Indexed libraries were quantified, pooled and sequenced on NextSeq Illumina platform.

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University of Tasmania EBV-MS Data Sharing Acknowledgment

The below acknowledgment refers to data submitted to the European Genome-Phenome Archive (EGA) for controlled access by persons, institutions or organisations in line with the details below. Individuals may contact Dr Yuan Zhou, Yuan.Zhou@utas.edu.au with specific enquiries. DATA SHARING ACKNOWLEDGMENT   1. DEFINITIONS “Accessor” means the person, institution or organisation that is accessing the Data provided by UTAS to the repository. “Confidential Information” means any private or personal information about the study participants involved in generation of the Data and the Data. “Consequential Loss" means any indirect, incidental, consequential or special loss, whether or not such loss was reasonably in the contemplation of a party, including any loss of profits, loss of revenue, loss of sales, loss of business, business interruption, loss of data, loss of contracts, loss of opportunity, loss of reputation, loss of goodwill, loss of anticipated savings, or similar loss or damage. “Data” means the DNA or RNA sequencing data that UTAS has provided to the repository. “Derived Data” means the outcome of analyses performed by the Accessor using the Data that UTAS has provided to the repository. “Ethics Committee” means the University’s committees on animal ethics that oversees the care and use of animals in research and teaching, human research ethics that reviews research proposals involving human participants, and any other ethics committee established by the University. “Intellectual Property” means all copyright and neighbouring rights, all rights in relation to inventions (including patent rights), patents, plant varieties, registered and unregistered trade marks (including service marks), registered designs, confidential information (including trade secrets and know-how and circuit layouts), and all other rights resulting from intellectual activity in the industrial, scientific, literary or artistic fields (other than Moral Rights under the Copyright Act 1968 (Cth)). “Research” means the creation of new knowledge and/or the use of existing knowledge in a new and creative way to generate new concepts, methodologies, inventions and understandings. This could include synthesis and analysis of previous research to the extent that it is new and creative. “Permitted Use” means use of the Data for research. “UTAS” means the University of Tasmania and owner of the Data 2. CONFIDENTIAL INFORMATION 2.1. The Accessor agree that all Confidential Information disclosed by UTAS to the Accessor, whether existing prior to the commencement of the Acknowledgement or created is confidential and shall be kept confidential and shall not be disclosed to any other Party or any third party without the prior written consent of UTAS (such consent not to be unreasonably withheld or delayed), except where disclosure is: (a) required by law; (b) of information in the public domain other than due to a breach of this clause; or (c) required for the Purpose, and then only on prior written notice to the disclosing party. 2.2. If the Accessor is required to disclose confidential information in line with clause 2.1(a) they are obligated to contact UTAS. UTAS retain the right to limit the disclosure to what is required only. 2.3. The Assessor must ensure that any disclosure to a third party is on equivalent confidentiality terms as those contained within this clause. 3. PRIVACY & PERSONAL INFORMATION The Accessor agrees to: (a) Use personal information, as defined in the Personal Information Protection Act 2004 (Tas) (PIP Act (Tas)) (“Personal Information”), obtained for the Permitted Use in accordance with the PIP Act (Tas) and applicable State privacy legislation (PIP Act (Tas)); (b) Comply with all applicable Australian Privacy Principles contained in the PIP Act (Tas) governing the collection, security, access, data quality, relevance, use and disclosure of Personal Information (including outside Australia) to the extent that those principles apply to this Acknowledgement; (c) ensure that any person (including the Accessor’s personnel and subcontractors) who has access to any personal information is made aware of, and undertakes to observe, all applicable Australian Privacy Principles; and (d) take all reasonable measures to ensure that personal information is protected against loss and unauthorised access, use, modification, disclosure, or other misuse and that only authorised personnel have access to the information. 4. DATA BREACH 4.1. Where UTAS identifies: (a) an actual or suspected Eligible Data Breach (as defined in the PIP Act (Tas); or (b) an actual or suspected unauthorised access or disclosure of Personal Information or loss of Personal Information provided by UTAS and which has been accessed or held by the Accessor for the purposes of the Permitted Use ((a) and (b) together a Breach), the Accessor agrees: (i) to immediately take any measures necessary to prevent the recurrence or continuation of the Breach and notify UTAS of the Breach including: (A) full details of the manner in which the Breach occurred; (B) the type of information affected by the Breach; and (C) any security measures applied to the Personal Information affected by the Breach; (ii) to assist and cooperate in investigating any Breach; (iii) unless otherwise agreed, to carry out an assessment in accordance with the requirements of the PIP Act (Tas); (iv) to take all reasonable action to mitigate the risk of the Breach causing serious harm to any of the individuals to whom the Data relates; (v) to provide all information reasonably requested by UTAS in connection with the Breach; and (vi) that UTAS will be the sole person responsible for making any notification of that Breach required by law, unless otherwise agreed between the Parties. 5. INTELLECTUAL PROPERTY 5.1. Both UTAS and the Accessor agree that the ownership of Intellectual Property is not affected by this Acknowledgement; that all Intellectual Property related to the Data remains the property UTAS, and that UTAS makes it available for the Permitted Use. 5.2. UTAS grants the Accessor a royalty-free, non-exclusive, non-transferable, non-sub licensable licence to use its Intellectual Property to the extent necessary to carry out the Permitted Use. 5.3. No representations or warranties are made or given in relation to Intellectual Property, however each Party providing Intellectual Property, acknowledges that to the best of its knowledge, without the need to make additional enquiries, conduct searches or seek a legal opinion, such Intellectual Property when used in accordance with this Acknowledgement will not infringe any third-party Intellectual Property rights. 6. LIABILITY 6.1. Consequential Loss Neither UTAS or the Accessor will be liable to the other in any circumstances for any Consequential Loss which UTAS or the Accessor suffers as a result of any act or omission by the other under this Acknowledgement. 7. PERMITTED USES OF DATA AND DERIVED DATA 7.1. UTAS grants to the Accessor a right to use the Data and Derived Data for the Permitted Use. 7.2. UTAS agree and acknowledge that the Derived Data vests in the Accessor upon creation. 7.3. The Permitted Use excludes the following: (a) use of the Data for a commercial purpose; (b) identifying, or attempting to identify, individual participants from whom the Data or Derived Data was obtained or derived; (c) using Data or Derived Data in a manner that is inconsistent or contrary to applicable federal and state laws and regulations, or indigenous law or custom; (d) selling, providing, or providing access to, the Data or Derived Data to a third party or to any person who does not reasonably require access in order to perform the Research; (e) using the Data or Derived Data in a way which will, or could, have the effect of infringing human rights, fundamental freedoms or human dignity of an individual or for purposes that lead to the stigmatization of an individual, a family, a group or a community; or (f) any use that is contrary to the conditions under which an Ethics Committee has provided approval for the User to conduct the Research. 8. PUBLICATION 8.1. UTAS provides consent for the Accessor to publish without restriction provided a copy of any pending publication is sent to Yuan.Zhou@utas.edu.au and all other conditions of the Acknowledgement are met. 8.2. The Accessor will cite the original research paper prepared by UTAS and accession number as the source of the Data in all publications. 8.3. The Accessor will ensure that Confidential Information is only provided in a deidentified or group format or provided by citing the Data source and original research paper. 9. GENERAL 9.1. The Assessor must not assign its rights or obligations under this Acknowledgement without the prior written consent of UTAS. 9.2. This Acknowledgement constitutes the entire Acknowledgement between the UTAS and the Accessor in relation to its subject matter and supersedes any previous Agreement or Acknowledgement, or any other communication or representation made, in relation to its subject matter. 9.3. UTAS and the Accessor must do or cause to be done all acts and things necessary or desirable to give effect to this Acknowledgement and must refrain from doing all acts and things that could hinder performance of this Acknowledgement. 9.4. This Acknowledgement is governed by and must be construed in accordance with the laws of Tasmania, Australia. The Accessor irrevocably and unconditionally submits to the non-exclusive jurisdiction of the courts of Tasmania, Australia and all courts that have jurisdiction to hear appeals from them and waives any right to object to proceedings being brought in those courts for any reason.

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
EGAS00001008518 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
EGAF00009247623 fastq.gz 722.2 MB
EGAF00009247624 fastq.gz 373.6 MB
EGAF00009247625 fastq.gz 665.5 MB
EGAF00009247626 fastq.gz 509.7 MB
EGAF00009247627 fastq.gz 344.9 MB
EGAF00009247628 fastq.gz 500.5 MB
EGAF00009247629 fastq.gz 1.2 GB
EGAF00009247630 fastq.gz 911.5 MB
EGAF00009247631 fastq.gz 2.2 GB
EGAF00009247632 fastq.gz 1.2 GB
EGAF00009247633 fastq.gz 2.1 GB
EGAF00009247634 fastq.gz 1.8 GB
EGAF00009247635 fastq.gz 1.7 GB
EGAF00009247636 fastq.gz 1.1 GB
EGAF00009247637 fastq.gz 2.6 GB
EGAF00009247638 fastq.gz 2.5 GB
EGAF00009247639 fastq.gz 4.3 GB
EGAF00009247640 fastq.gz 5.1 GB
EGAF00009247641 fastq.gz 4.5 GB
EGAF00009247642 fastq.gz 972.4 MB
EGAF00009247643 fastq.gz 5.2 GB
EGAF00009247644 fastq.gz 10.3 GB
EGAF00009247645 fastq.gz 1.1 GB
EGAF00009247646 fastq.gz 9.8 GB
24 Files (61.7 GB)