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ADT/SPEX CITE-Seq performance dataset

To understand the impact of enzymatic treatments on gene expression and epitope preservation on major immune cell populations, skin dissociation (SkinD) and solid soft tumor dissociation (TumorD) were tested on three healthy PBMC samples in triplicate (D1, D2, D3), against an untreated control. CITE-seq performance was assessed on a solid biopsy cohort of 11 samples (5 healthy skin samples, 3 primary melanoma samples, 3 melanoma metastasis samples) as well as on a liquid biopsy PBMC cohort consisting of three healthy donors and three immunotherapy-treated melanoma patients. This dataset contains the ADT/SPEX data for each sample. Data is provided in the form of pooled BAM files. Linkage between samples, BAM files and hashtags is provided in a separate linkage file.

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Citeseq policy

Contact and Project Information A. Data Recipient (including contact details) Please ensure that a full postal address and a valid Institutional email address are included Name: Institution’s Legal Name: Institutional Postal Address: Institutional E-mail Address: Website of the Institution: B. Authorised Representative of the Data Recipient Name: Position: Affiliation: Institutional Postal Address: Institutional E-mail Address: C. Data Controller(s) (including contact details) Please ensure that a full postal address and a valid Institutional email address are included Name: Dr. Mitchell Levesque Position: Associate Professor Affiliation: University of Zürich Hospital, Department of Dermatology Institutional Postal Address: Wagistrasse 18, 8952, Schlieren, Zurich, Switzerland Institutional E-mail Address: mithchell.levesque@usz.ch Name: Dr. Christian Beisel Position: Head Genomics Facility Basel Affiliation: Department of Biosystems Science and Engineering, ETHZ Institutional Postal Address: Mattenstrasse 26, 4058 Basel, Switzerland Institutional E-mail Address: christian.beisel@bsse.ethz.ch D. Authorised Representative of the Data Controller(s) Name: Patrick Turko Position: Bioinformatician Affiliation: University of Zürich Hospital, Department of Dermatology Institutional Postal Address: Wagistrasse 18, 8952, Schlieren, Zurich Institutional E-mail Address: Patrick.Turko@usz.ch E. Requested Data Study ID: EGAS00001005849 Study Title: “Optimisation of CITE-seq on liquid and solid tissues” F. Title of the Proposed Research Project G. Research Project (Scientific Abstract): Please provide a clear description of the Project, its stakeholders, its main question and its relevance to the research domain addressed, its specific aims, and duration. Note that any use of the Data, if approved, must fall under the framework of the described Project (300 words max): H. Research Credentials Please provide a list of three Publications, relevant to the Project description, of which the Data Recipient is author or co-author, and, also, attach their (Data Recipient’s) short CV. If the Data Recipient has not authored or co-authored three relevant Publications, please describe their relevant expertise or experience in no more than 150 words; also, notify how the research project will be carried out (e.g. available funding, infrastructure and so on). Harmonised Data Access Agreement (hDAA) Definitions GDPR: This hDAA makes both parties compliant with the Regulation (EU) 2016/679 of the European Parliament and of the Council, that is, the General Data Protection Regulation (herein referred to as the ‘GDPR’). Data: Refers to controlled access data (the Data). Under this Agreement, the Data is pseudonymised. Data Access/Transfer: Refers to an Institution’s right to request access to the Data and retrieve them from the Data Controller’s Institution upon approval of this hDAA by the corresponding DAC within the Data Controller’s Institution. Data Handling: Refers to an Institution’s ability to analyse and manipulate the Data within its own computer network. Data Controller(s): Refers to an Institution, responsible for the generation of the Data and its pseudonymisation. A key-code permitting relinkage to Data Subjects is kept by the Data Controller(s). Data Subject: Refers to any individual who is the source of any Data covered by this Agreement. Data Recipient (‘You’): Refers to the Institution who requests Access to the Data through this Agreement. Authorised Personnel: The individual(s) at the Institution requesting Access to the Data. Research Project: The Project for which You have requested Access to the Data. Publications: Refers, without limitation, to any and all articles published in print journals, electronic journals, reviews, books, posters, and other written and verbal presentations of Research that have been accepted by peer review. EU-STANDS4PM: This hDAA was developed by the EU-STANDS4PM, http://www/eu-stands4pm.eu/ Terms and Conditions In signing this Agreement: 1. You, the Data Recipient, agree to only use the Data for the Purpose of the Project. 2. You agree to use the data only for the advancement of medical research, according to the consent obtained from sample donors. 3. You agree not to use the data for the creation of products for sale or for any commercial purpose. 4. You agree to preserve, at all times, the confidentiality of information and Data pertaining to Data Subjects. In particular, you undertake not to use, or attempt to use the Data to compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy. 5. You agree not to transfer or disclose the data, in whole or part, or any identifiable material derived from the Data, to others, except as necessary for data/safety monitoring or program management. Should you wish to share the Data with a collaborator, the third party must make a separate application for access to the data. 6. You and your Authorised Personnel agree to take into consideration any usage restrictions (if any), stemming from consent, i.e. the appropriate lawful basis for processing the Data, as well as any usage restrictions stemming from any applicable internal policies of your Institution. 7. You agree that in handling this Data You will follow an up-to-date information technology (IT) policy that must include, at a minimum, the following items: a. Logging and auditing of Access to the Data and to the computer network; b. Password protection to computer network and/or strong data encryption; c. Virus and malware protection to computers on the computer network; d. Secure backup procedure; 8. You agree to use the data for the approved purpose and project described in your application; use of the data for a new purpose or project will require a new application and approval. 9. You recognize that nothing in this Agreement shall operate to transfer to You any intellectual property rights to the Data. 10. You agree not to make intellectual property claims on the Data and not to use intellectual property protection in ways that would prevent or block Access to, or use of, any element of the Data. 11. You agree to acknowledge in any work based in whole or part on the data, the published paper from which the data derives, and the repository it was obtained from. 12. You agree to acknowledge the contribution of the Data Controller(s) in all oral and written presentations, disclosures, and Publications resulting from all analyses of the Data. 13. You accept that the Data Access Committee, the original data creators, depositors or copyright holders, or the funders of the data or any part of the data supplied: a) bear no legal responsibility for the accuracy or comprehensiveness of the data; and b) accept no liability for indirect, consequential, or incidental, damages or losses arising from use of the data, or from the unavailability of, or break in access to, the data for whatever reason. 14. You understand and acknowledge that the data is protected by copyright and other intellectual property rights, and that duplication, except as reasonably required to carry out your research with the data, or sale of all or part of the data on any media is not permitted. 15. You agree that the Research Project 1) bears no legal responsibility for the accuracy or comprehensiveness of the Data; 2) accepts no liability for indirect, consequential, or incidental damages or losses arising from use of the Data; and 3) bears no responsibility for the further analysis or interpretation of these Data over and above that published by the Controller(s). 16. You agree to hold the Data Subject(s) and Data Controller(s) harmless and to defend and indemnify all these parties against all liabilities, demands, damages, expenses, and losses arising out of Your use for any Purpose of the Data. 17. You agree to use the Data in Your laboratory. Any Authorised Personnel shall work under Your direct supervision. You agree to distribute a copy of these terms to the Authorised Personnel. 18. You accept that it may be necessary for the Data Access Committee or its appointed agent to alter the terms of this agreement from time to time in order to address new concerns. In this event, the Data Access Committee or its appointed agent will contact you to inform you of any changes and you agree that your continued use of the data shall be dependent on the parties entering into a new version of the Agreement. 19. You agree that you will submit a report to the Data Access Committee, if requested, on completion of the agreed purpose. The Data Access Committee agrees to treat the report and all information, data, results, and conclusions contained within such report as confidential information belonging to the Data Recipient. 20. You shall ensure that ‘all’ who have Access to the Data, namely You and Your Authorised Personnel, will be listed out, and are made aware and be bound by the terms of this Agreement. You remain solely and fully responsible for Your Authorised Personnel’s non-compliance with the provision of the Agreement and/or applicable laws. 21. In case of a breach of security resulting from ‘accidental’ use of Data by You and Your Authorised Personnel, which leads to disclosure of Data, then You must report this to Data Controller(s) within 72 hours maximum, and follow any relevant rule as provided by the GDPR. 22. In case of a ‘non-accidental or minor’ breach of hDAA by You You will further be required to destroy any Data held. 23. You accept that this Agreement will terminate immediately upon ‘any’ breach by You, or its termination (see Section I). 24. You accept that the data is protected by and subject to international laws, including but not limited to the Swiss Human Research Act, and that you are responsible for ensuring compliance with any such applicable law. The Data Access Committee reserves the right to request and inspect data security and management documentation to ensure the adequacy of data protection measures in countries that have no national laws comparable to that which pertain in the EAA. 25. This agreement shall be construed, interpreted and governed by the laws of Switzerland and shall be subject to the non-exclusive jurisdiction of Swiss courts. Agreement I have read, understood and agree to abide by the terms and conditions stipulated in this Data Access Agreement. Data Recipient or Authorised Representative of the Data Recipient: Name: Title and position (if applicable): Affiliation (if applicable): Signature: _____________________________________Date: _____________________ Data Controller(s) or Authorised Representative of the Data Controller(s): Name: Title and position (if applicable): Affiliation (if applicable): Signature: _____________________________________Date: ______________________

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
EGAS00001005849 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
EGAF00005740396 bam 9.6 GB
EGAF00005740398 bam 9.8 GB
EGAF00005740399 bam 5.9 GB
EGAF00005740401 bam 14.4 GB
EGAF00005740403 bam 2.4 GB
EGAF00005740405 bam 2.5 GB
EGAF00005740406 bam 9.6 GB
EGAF00005740410 bam 7.7 GB
EGAF00005740411 bam 8.6 GB
EGAF00005740413 bam 15.3 GB
10 Files (85.8 GB)