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scRNA-seq and scTCR-seq from 7 MF patients

Dataset containing scRNA and scTCR sequencing of 7 patients with cutaneous T cell lymphoma. Sequencing was performed on Illumina NextSeq 550, HiSeq 4000 and NovaSeq 6000. The sequencing was always paired.

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DAP for "Combined single-cell transcriptomics and T-cell receptor sequencing reveal heterogeneity of mycosis fungoides between and within patients and identify a CD4+ cytotoxic subtype"

Data Transfer Agreement of Human Genomic Data for Research Purposes Between: (1) Deutsches Krebsforschungszentrum (DKFZ), Stiftung des öffentlichen Rechts, legally represented by its Management Board , Prof. Dr. med. Michael Baumann and Ursula Weyrich Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany (“PROVIDER“) and (2) [INSERT INSTITUTION DETAILS] (“RECIPIENT”). 1 Preamble Public genetic sequence databases are a critical part of our academic biomedical research infrastructure. However, human genetic data should only be made public if we can adequately protect the privacy of research subjects. Individual genomic sequence data are sensitive patient data and any attempt to re-identify such data is forbidden under any circumstances. Our efforts to understand disease susceptibility or therapeutic opportunity require access to large genomic data sets. Therefore, the special privacy challenges posed by genomic data are addressed by PROVIDER with this Agreement. In response to the RECIPIENT's request for access to the DATA (as defined below), PROVIDER and the RECIPIENT agree as follows: 2 Definitions “DATA” shall mean all and any human genetic data obtained by the RECIPIENT from the PROVIDER including the Data Subjects’ e.g. age, sex and tumor pathology (as listed in Annex 2). For the avoidance of doubt, Data does not include samples or biological materials; “DATA SUBJECT” shall mean the person (irrespective of the state of health) to whom Data refers and who has been informed of the purpose for which the Data is held and has given his/her informed consent thereto; “COMMERCIAL PURPOSES” shall mean the sale, lease, license, or other transfer and/or the use of the DATA to and/or by a for-profit organization. However, industrially sponsored academic research shall not be considered a use of the DATA for Commercial Purposes per se. “INTELLECTUAL PROPERTY” shall mean (i) patents, designs, trademarks and trade names (whether registered or unregistered), copyright and related rights, database rights, know-how and confidential information; (ii) all other intellectual property rights and similar or equivalent rights (whether registered or unregistered and whether registrable or unregistrable) anywhere in the world which currently exist or are recognized in the future; and (iii) applications, extensions and renewals in relation to any such rights; “RECIPIENT SCIENTIST” shall mean a researcher (or an individual conducting Research under the supervision of a researcher) that is employed by the RECIPIENT and is bound by confidentiality and non-use obligations in respect of DATA and who has accepted the terms of this Agreement in writing (however, for the avoidance of doubt, without being a party to this Agreement) and has received acknowledgement of its acceptance. For the avoidance of doubt and without having explicitly accepted the terms of this Agreement in writing, “RECIPIENT SCIENTIST” may also include any other RECIPIENT’s employees, students, visiting academics, contractors, sub-contractors or independent consultants provided that any of such latter individuals is bound by confidentiality and non- use obligations no less onerous than those binding the RECIPIENT’s employees; “RESEARCH” shall mean research that is seeking to advance the understanding and treatment of cancer and closely related diseases, and work on statistical methods that may be applied to such research; “PROJECT” shall mean a detailed description as in Annex 3; 3 Purpose of the Project The RECIPIENT agrees to use DATA only for RESEARCH as described in the purpose of the PROJECT (Annex 3). 4 Confidentiality The RECIPIENT agrees to preserve, at all times, the confidentiality of DATA pertaining to DATA SUBJECTs. In particular, the RECIPIENT undertakes not to use, or attempt to use the DATA to deliberately compromise or otherwise infringe the confidentiality of information on DATA SUBJECTs and their respective rights to privacy. 5 DATA Protection The Recipient and its RECIPIENT SCIENTIST are covered by and the RECIPIENT shall, and shall procure that its RECIPIENT SCIENTISTS shall, comply with the obligations contained in the applicable German and EU data protection laws and regulations as amended from time to time. In particular, the RECIPIENT and its RECIPIENT SCIENTISTs inter alia understands, and shall procure that its RECIPIENT SCIENTISTs understand, their duties under the German and EU legislation in relation to the handling of DATA and the rights of DATA SUBJECTs. The RECIPIENT agrees that it, and its RECIPIENT SCIENTISTs, shall not analyze or make any use of the DATA in such a way that has the potential to: a) lead to the re-identification of any DATA SUBJECT; or b) compromise the anonymity of any DATA SUBJECT in any way. The RECIPIENT shall, and it shall procure that its RECIPIENT SCIENTISTS shall, adhere to the principles of IT-Security as set forth in Annex 1 hereto. 6 Access and Governance The RECIPIENT agrees that it shall take all (commercially) reasonable security precautions to keep the DATA confidential, such precautions to be no less onerous than in the applicable German and EU data protection laws and regulations. The RECIPIENT agrees to use the DATA solely for RESEARCH in the frame of the purpose of the PROJECT. The RECIPIENT agrees that the DATA shall not be distributed or released to any other location and/or to any other person other than RECIPIENT SCIENTISTs or laboratory personnel under the RECIPIENT SCIENTISTs direct supervision. RECIPIENT does not have the right to sublicense the DATA. RECIPIENT shall inform PROVIDER about any third party requests for the DATA. PROVIDER reserves the right to request and inspect DATA security and management documentation at the RECIPIENT’s premises to ensure the adequacy of DATA protection measures with prior notice during the RECIPIENT’s ordinary working hours. DATA shall not be used for COMMERCIAL PURPOSES (e.g. diagnostic services). In case of intended commercial use of DATA, the RECIPIENT shall start negotiations in good faith leading to a fair market compensation of PROVIDER. Such a disclosure of DATA shall require a binding declaration of consent in writing from the person concerned. 7 Errors The RECIPIENT agrees to notify the PROVIDER of any errors detected in the DATA without undue delay. 8 DATA reissue The RECIPIENT accepts that PROVIDER will reissue DATA from time to time, with suitable versioning. If DATA is reissued at the request of the DATA SUBJECT and/or as the result of other ethical scrutiny, the RECIPIENT agrees to destroy all earlier versions of the DATA without undue delay once he has received such information. This shall not apply to the extent that DATA is saved in automatic back-up systems for which destruction shall follow the regular process of such back-up system, however, such DATA shall be eliminated within a period of four (4) weeks after reception of the respective request to do so or within a period of four (4) weeks upon termination in accordance with this Agreement. 9 INTELLECTUAL PROPERTY The RECIPIENT recognizes that nothing in this Agreement shall operate to transfer to the RECIPIENT or its RECIPIENT SCIENTISTs any INTELLECTUAL PROPERTY rights in or relating to the DATA, i.e. ownership of DATA remains unchanged. The RECIPIENT does not have the right to sublicense the DATA. The RECIPIENT shall inform PROVIDER about any third party requests for the DATA. In case the RECIPIENT and its RECIPIENT SCIENTISTs develops INTELLECTUAL PROPERTY based on or related to DATA as set forth in this Agreement the RECIPIENT shall become owner of such results. The RECIPIENT will inform PROVIDER about all developed INTELLECTUAL PROPERTY based on or related to DATA as set forth in this Agreement without undue delay in writing. The RECIPIENT grants PROVIDER a non-exclusive, non-transferable, royalty-free, perpetual, non-sublicensable right to use such developed INTELLECTUAL PROPERTY for internal research purposes including collaborations with any third parties excluding any COMMERCIAL PURPOSES. 10 Publications The RECIPIENT agrees to acknowledge in any RECIPIENT’s work based in whole or part on the DATA, any PROVIDER publications which encompass and from which DATA derive, the respective version of the DATA obtained, and the role of PROVIDER. The RECIPIENT is also entitled to release publications and, in doing so, agrees to acknowledge any of PROVIDER’s work based in whole or part on the DATA in its publication. The RECIPIENT will also declare in any such work that PROVIDER and its employees bear no responsibility for the further analysis or interpretation of the DATA by the RECIPIENT. 11 Violation/Termination of Agreement This Agreement shall expire automatically three (3) years after its signature by both parties. This Agreement will terminate immediately upon any material breach of a provision of this Agreement. The RECIPIENT accepts that the changing ethical framework of human genetic research may lead to: (i) alteration to the provisions of this Agreement, in which case the RECIPIENT may accept such alterations or terminate this Agreement; or (ii) the withdrawal of this Agreement in extreme circumstances. Either party shall have the right to terminate this Agreement with immediate effect upon giving written notice of termination to the other party. In the event that this Agreement is expired the RECIPIENT is required to destroy/discard any Data held, including but not limited to copies and backup copies. This shall not apply to the extent that DATA is saved in automatic back-up systems for which destruction shall follow the regular process of such back-up system, however, such DATA shall be eliminated within a period of four (4) weeks after the date of termination. Upon request of PROVIDER, the RECIPIENT will certify the destruction of the DATA. Sections 4, 5, 9 and 10 of this Agreement remain in full force and effect in case of termination. Notwithstanding the aforementioned, any provision of this Agreement related to confidentiality and/or DATA protection shall survive the expiration of this Agreement to the extent applicable statutory law provides for a deviating period of validity and effectiveness. Nothing contained in this paragraph shall restrict the right of the PROVIDER to seek injunctive relief to prevent any breach or threatened breach of this agreement, furthermore nothing contained in this paragraph shall prohibit the PROVIDER from pursuing any other remedies available to it for such breach or threatened breach, including the recovery of damages from RECIPIENT.

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
EGAS50000000226 RNASeq

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
EGAF50000088566 fastq.gz 569.3 MB
EGAF50000088567 fastq.gz 609.3 MB
EGAF50000088568 fastq.gz 435.5 MB
EGAF50000088569 fastq.gz 483.3 MB
EGAF50000088570 fastq.gz 513.1 MB
EGAF50000088571 fastq.gz 461.3 MB
EGAF50000088572 fastq.gz 260.6 MB
EGAF50000088573 fastq.gz 280.4 MB
EGAF50000088574 fastq.gz 790.5 MB
EGAF50000088575 fastq.gz 745.2 MB
EGAF50000088576 fastq.gz 1.0 GB
EGAF50000088577 fastq.gz 971.2 MB
EGAF50000088578 fastq.gz 402.3 MB
EGAF50000088579 fastq.gz 444.5 MB
EGAF50000088580 fastq.gz 308.0 MB
EGAF50000088581 fastq.gz 340.3 MB
EGAF50000088582 fastq.gz 85.2 MB
EGAF50000088583 fastq.gz 85.4 MB
EGAF50000088584 fastq.gz 52.6 MB
EGAF50000088585 fastq.gz 51.2 MB
EGAF50000088586 fastq.gz 58.3 MB
EGAF50000088587 fastq.gz 56.6 MB
EGAF50000088588 fastq.gz 84.5 MB
EGAF50000088589 fastq.gz 86.9 MB
EGAF50000088590 fastq.gz 467.3 MB
EGAF50000088591 fastq.gz 379.4 MB
EGAF50000088592 fastq.gz 560.9 MB
EGAF50000088593 fastq.gz 455.4 MB
EGAF50000088594 fastq.gz 437.7 MB
EGAF50000088595 fastq.gz 362.4 MB
EGAF50000088596 fastq.gz 4.2 GB
EGAF50000088597 fastq.gz 1.6 GB
EGAF50000088598 fastq.gz 479.4 MB
EGAF50000088599 fastq.gz 386.4 MB
EGAF50000088600 fastq.gz 88.2 MB
EGAF50000088601 fastq.gz 101.4 MB
EGAF50000088602 fastq.gz 102.2 MB
EGAF50000088603 fastq.gz 89.0 MB
EGAF50000088604 fastq.gz 529.3 MB
EGAF50000088605 fastq.gz 521.1 MB
EGAF50000088606 fastq.gz 881.4 MB
EGAF50000088607 fastq.gz 849.5 MB
EGAF50000088608 fastq.gz 80.2 MB
EGAF50000088609 fastq.gz 90.3 MB
EGAF50000088610 fastq.gz 125.0 MB
EGAF50000088611 fastq.gz 109.2 MB
EGAF50000088612 fastq.gz 8.8 GB
EGAF50000088613 fastq.gz 3.5 GB
EGAF50000088614 fastq.gz 3.5 GB
EGAF50000088615 fastq.gz 8.7 GB
EGAF50000088616 fastq.gz 5.9 GB
EGAF50000088617 fastq.gz 15.1 GB
EGAF50000088618 fastq.gz 236.6 MB
EGAF50000088619 fastq.gz 481.9 MB
EGAF50000088620 fastq.gz 3.9 GB
EGAF50000088621 fastq.gz 11.3 GB
EGAF50000088622 fastq.gz 214.5 MB
EGAF50000088623 fastq.gz 438.2 MB
EGAF50000088624 fastq.gz 281.0 MB
EGAF50000088625 fastq.gz 579.1 MB
EGAF50000088626 fastq.gz 2.7 GB
EGAF50000088627 fastq.gz 7.8 GB
EGAF50000088628 fastq.gz 2.4 GB
EGAF50000088629 fastq.gz 5.8 GB
EGAF50000088630 fastq.gz 3.9 GB
EGAF50000088631 fastq.gz 1.6 GB
EGAF50000088632 fastq.gz 1.9 GB
EGAF50000088633 fastq.gz 4.6 GB
EGAF50000088634 fastq.gz 1.8 GB
EGAF50000088635 fastq.gz 4.4 GB
EGAF50000088636 fastq.gz 997.3 MB
EGAF50000088637 fastq.gz 2.6 GB
EGAF50000088638 fastq.gz 1.3 GB
EGAF50000088639 fastq.gz 3.4 GB
EGAF50000088640 fastq.gz 2.3 GB
EGAF50000088641 fastq.gz 884.6 MB
EGAF50000088642 fastq.gz 1.3 GB
EGAF50000088643 fastq.gz 3.4 GB
EGAF50000088644 fastq.gz 1.1 GB
EGAF50000088645 fastq.gz 3.0 GB
EGAF50000088646 fastq.gz 3.9 GB
EGAF50000088647 fastq.gz 1.5 GB
EGAF50000088648 fastq.gz 1.7 GB
EGAF50000088649 fastq.gz 4.6 GB
EGAF50000088650 fastq.gz 3.8 GB
EGAF50000088651 fastq.gz 1.4 GB
EGAF50000088652 fastq.gz 2.2 GB
EGAF50000088653 fastq.gz 6.3 GB
EGAF50000088654 fastq.gz 2.4 GB
EGAF50000088655 fastq.gz 6.9 GB
EGAF50000088656 fastq.gz 236.9 MB
EGAF50000088657 fastq.gz 486.5 MB
EGAF50000088658 fastq.gz 2.4 GB
EGAF50000088659 fastq.gz 891.2 MB
EGAF50000088660 fastq.gz 3.2 GB
EGAF50000088661 fastq.gz 1.2 GB
EGAF50000088662 fastq.gz 1.6 GB
EGAF50000088663 fastq.gz 4.3 GB
EGAF50000088664 fastq.gz 100.7 MB
EGAF50000088665 fastq.gz 85.0 MB
EGAF50000088666 fastq.gz 84.0 MB
EGAF50000088667 fastq.gz 71.6 MB
EGAF50000088668 fastq.gz 289.0 MB
EGAF50000088669 fastq.gz 322.3 MB
EGAF50000088670 fastq.gz 200.6 MB
EGAF50000088671 fastq.gz 224.9 MB
EGAF50000088672 fastq.gz 103.7 MB
EGAF50000088673 fastq.gz 95.4 MB
EGAF50000088674 fastq.gz 68.9 MB
EGAF50000088675 fastq.gz 58.6 MB
110 Files (193.1 GB)