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Illumina_WXS_T-XEN-CELL

Whole-exome sequencing on Illumina HiSeq2000/2500 of PDO culture derived from Patient-derived xenograft derived from colorectal cancer primary tumor sample

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Oncotrack policy

Data and Sample Transfer Agreement for Research Purposes between (1) [INSERT: OncoTrack Partner responsible for subcontract] (“PROVIDER”) 1 and (2) [INSERT INSTITUTION DETAILS] (“RECIPIENT”). (PROVIDER and RECIPIENT hereinafter jointly referred to as the “PARTIES” and each a “PARTY”) Preamble WHEREAS, PROVIDER is the owner of certain patient data and/or patient samples collected in the context of PROVIDER’s participation in the Innovative Medicines Initiative (IMI) OncoTrack project on “Methods for systematic next generation oncology biomarker development,” as stipulated in the OncoTrack Project Agreement (“OncoTrack Project Agreement”) and wishes to share such data and/or samples with RECIPIENT for a predefined research purpose; and WHEREAS, RECIPIENT desires to get access to and obtain a license to use PROVIDER’s data and/or samples in order to conduct non-commercial research activities aiming at [please describe the goal of the research, and see Annex 3]; NOW, THEREFORE, in consideration of mutual promises, PROVIDER and RECIPIENT agree as follows In response to the RECIPIENT's request for access to the DATA and/or SAMPLES, PROVIDER and the RECIPIENT agree as follows: 1 Definitions “DATA” shall mean the patient data provided by PROVIDER to RECIPIENT including the Data Subjects’ e.g. age, sex, tumour pathology, genome sequencing and other molecular data (as listed in Annex 2). “DATA SUBJECT” shall mean the person (irrespective of the state of health) to whom Data and/or SAMPLES refer and who has been informed of the purpose for which the Data and/or SAMPLES is collected, stored, used and transferred; “COMMERCIAL PURPOSES” shall mean the sale, lease, license, or other transfer and/or the use of the DATA and/or SAMPLES to and/or by a for-profit organization. However, industrially sponsored academic research shall not be considered a use of the DATA and/or SAMPLES 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 1 Provider is the OncoTrack consortium member that is the owner of the DATA and/or SAMPLES. In case of joint ownership there may be more than one Provider. 1any such rights; “RECIPIENT SCIENTIST” shall mean a researcher (or an individual conducting RESEARCH) that is employed by the RECIPIENT and is bound by confidentiality and non-use obligations in respect of DATA and/or SAMPLES and who has acknowledged and agreed to 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 then those binding the RECIPIENT’s employees; “RESEARCH” shall mean research that is seeking to [please specify scope of research as described in Annex 3] and work on statistical methods that may be applied to such research; “SAMPLES” shall mean any human tissue or human biological material of a DATA SUBJECT, including any portion of an organ, any tissue, skin, bone, muscle, connective tissue, blood, cerebrospinal fluid, cells, gametes, or sub-cellular structures such as DNA, or any derivative of such human biological material such as stem cells, cell lines or xenograft tissues. “PROJECT” shall mean a detailed description as in Annex 3; “AFFILIATE” shall mean a person, corporation, firm, joint venture or other entity which, directly or indirectly, through one or more intermediates, is controlled by, controls, or is under common control with either of the PARTIES. As used in this definition “control” means possession of the power to direct or cause the direction of the management and policies of an entity, whether through the ownership of the outstanding voting securities or by contract or otherwise. 2 Purpose of the PROJECT PROVIDER hereby grants to RESEARCHER a one-time fully paid-up, royalty-free, non-exclusive, non-transferable license for use by RESEARCHER of the DATA and/or SAMPLES for the sole purpose of conducting the PROJECT and for no other purpose. This grant of a license shall not transfer any title or ownership rights in the DATA and/or SAMPLES, including any intellectual property embodied therein, which title and ownership rights shall at all times remain with PROVIDER. The license is granted on the express condition that, except as specifically authorized under this Agreement, no part or all of the DATA and/or SAMPLES shall be used by, made available to, or disclosed to any person or entity except as specifically set forth herein. The DATA and/or SAMPLES provided hereunder are provided ‘AS IS’ and PROVIDER makes no representations or warranties regarding the suitability of the DATA and/or SAMPLES provided to RECIPIENT for the PROJECT. The RECIPIENT shall not (i) transfer, reveal, market, sell, offer for sale lease, license, sublicense, loan, or otherwise provide the DATA and/or SAMPLES to any third party, whether or not such action is for commercial advantage, or (ii) create derivative works of, use, copy, modify, distribute, authorize the use of, publish, publicly perform, physically, optically, or digitally transmit, or display the whole or any portion of the DATA and/or SAMPLES, except as specifically authorized herein. 3 Confidentiality 2RECIPIENT agrees to treat all information and materials received from or on behalf of PROVIDER in the course of their cooperation, including the DATA and the SAMPLES (hereinafter collectively the “Information”) as strictly confidential both during the cooperation and after the expiration of this Agreement. RECIPIENT shall not use the Information for its own purposes or those of any third party. Nor will it disclose the Information to any other third party without obtaining the prior written consent of PROVIDER. RECIPIENT shall provide access to the Information only to such minimum number of its RECIPIENT SCIENTISTS with a need to know the Information for the purpose of this Agreement imposing on them restrictions on disclosure and use equivalent to those set out herein. The Information shall not be transferred to any third party without the prior written consent of PROVIDER. The obligation of confidentiality and non-use does not apply if RECIPIENT can demonstrate that the Information a) was already in its possession prior to the time of disclosure by PROVIDER, or b) was public knowledge at the time of disclosure by PROVIDER, or c) has become public knowledge other than through a breach of the Agreement on the part of RECIPIENT, or d) has been legally obtained by RECIPIENT by a third party who is not under a duty of confidentiality to PROVIDER, or e) was independently developed by RECIPIENT without reference to or use of the Information. Furthermore, RECIPIENT may disclose Information to the extent that such disclosure is required to comply with law or an enforceable judicial order, provided, however, that RECIPIENT shall give reasonable advance notice, as legally permissible, to PROVIDER and, at PROVIDER’s request, shall cooperate with PROVIDER to seek a protective order or other appropriate remedy. It shall use its reasonable efforts to secure confidential treatment of any Information that will be disclosed. Information will not be deemed to be or have become public knowledge merely because any part of such Information is embodied in general disclosures or because individual features, components or combinations of the Information are known or become known to the public. On completion of the Agreement, completion of the PROJECT or at any time at PROVIDER’s request, RECIPIENT shall immediately return to PROVIDER any Information or, at PROVIDER’s option, destroy such Information and promptly confirm destruction in writing. Return or destruction of the Information shall not affect CONTRACTOR’s obligation to keep the Information confidential pursuant to this Section 3. 4 DATA Protection The Recipient and its RECIPIENT SCIENTIST are subject to and the RECIPIENT shall, and shall procure that its RECIPIENT SCIENTISTS shall, comply with (i) the applicable German and EU data protection laws rules, guidelines and regulations as amended from time to time including the EU Data Protection Directive 95/46/EC and the Standards for Individually Identifiable Health Information, 42 C.F.R. §§ 160 and 164 (the "HIPAA Privacy Regulation") promulgated pursuant to the Health Insurance Portability and Accountability Act of 1996 as updated from time to time ("Data Protection Legislation") as well as (ii) the terms of this Agreement. 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/or SAMPLES and the rights of DATA SUBJECTs. 3The RECIPIENT agrees that it, and its RECIPIENT SCIENTISTs, shall not analyze or make any use of the DATA and/or SAMPLES 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. PROVIDER confirms that the DATA SUBJECTS’ informed consents for the DATA and/or SAMPLES are in full force and effect and allow the DATA and/or SAMPLE transfer to the RECIPIENT: 5 Access and Governance The RECIPIENT agrees that it shall take all (commercially) reasonable security precautions to keep the DATA and/or SAMPLES 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 and/or SAMPLES solely for RESEARCH in the frame of the purpose of the PROJECT. The RECIPIENT shall store the DATA and/or SAMPLES in a secure environment and strictly separated from his/her own data unless the PROJECT requires otherwise pooling of the DATA and/or SAMPLES with RECIPIENT’s own data. Notwithstanding the foregoing, RECIPIENT shall keep the pooled data in a secure environment and separate from his/her own data outside the PROJECT. RECIPIENT shall only grant access rights to this secure environment for RECIPIENT SCIENTISTS or laboratory personnel under the RECIPIENT SCIENTISTs direct supervision directly involved in the PROJECT and ensure that these personnel are bound to confidentiality obligations that provide the same level of safety as the provisions set forth in this Agreement. The RECIPIENT agrees that the DATA and/or SAMPLES 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 and/or SAMPLES. RECIPIENT shall inform PROVIDER about any third party requests for the DATA and/or SAMPLES. PROVIDER reserves the right to request and inspect DATA and/or SAMPLES 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 and/or SAMPLES shall not be used for COMMERCIAL PURPOSES (e.g. diagnostic services). In case of intended COMMERCIAL PURPOSES of DATA and/or SAMPLES, the RECIPIENT shall start negotiations in good faith leading to a fair market compensation of PROVIDER. Such a disclosure of DATA and/or SAMPLES for COMMERCIAL PURPOSES shall require a binding informed consent in writing from the DATA SUBJECT concerned. 6 Errors The RECIPIENT agrees to notify the PROVIDER of any errors detected in the DATA 4and/or SAMPLES without undue delay. 7 RESULTS and INVENTIONS The RECIPIENT recognizes that nothing in this Agreement shall operate to transfer to the RECIPIENT or to its RECIPIENT SCIENTISTs any INTELLECTUAL PROPERTY rights in or relating to the DATA and/or SAMPLES, i.e. ownership of DATA and/or SAMPLES remains unchanged. The RECIPIENT and PROVIDER shall have an equal, undivided interest in any result generated during the PROJECT, including any invention and any patent thereon (hereinafter the “Results”). The PARTIES shall take all measures to ensure such joint ownership. Upon an invention disclosure being received by RECIPIENT, RECIPIENT will notify PROVIDER immediately in writing of any Results. The PARTIES agree that RECIPIENT and PROVIDER shall be responsible for obtaining and maintaining patents on such jointly owned Results and shall share all expenses relating thereto. In the event of infringement by a third party of a jointly owned patent, either PARTY may assert such patent and initiate an action for infringement thereof, provided, however, that the other PARTY is given an opportunity in advance to join in the assertion and action and to share equally in the expenses and recoveries. Each PARTY agrees to cooperate and assist the other PARTY in any infringement action brought by the other PARTY in accordance with this provision, including joining the action to the extent necessary to permit the other PARTY to maintain the suit. The PARTIES shall not be entitled to assign or dispose of their interest in the Results without the prior written consent of the other PARTY, except that either PARTY may assign its interest in the Results to any of its AFFILIATES, provided that the AFFILIATE agrees to be bound by the provisions of this Agreement. Further, the PARTY shall not encumber their interest in the Results without the prior written consent of the other PARTY. The Results may be used by the PARTIES for the purposes of this Agreement, to the extent in compliance with the respective informed consent obtained. The PROVIDER may use the Results for non-COMMERCIAL PURPOSES. During the term of the OncoTrack Project, RECIPIENT may not use the Results with or on behalf of third parties, which are not members of the IMI OncoTrack Project or their affiliated entities, as provided for in the OncoTrack Project Agreement. During the term of the OncoTrack Project Agreement, RECIPIENT shall not be entitled to grant a license to such Results without the prior written consent of PROVIDER, which consent will not be unreasonably withheld taking into account the contractual commitments of PROVIDER under the OncoTrack Project Agreement. During the term of the OncoTrack Project Agreement, PROVIDER shall be entitled to grant licenses to such jointly owned Results to AFFILIATES, members of the OncoTrack Project and their affiliated entities, as provided for in the OncoTrack Project Agreement. After such term, both PARTIES shall be free to grant licenses without further restrictions, provided that this is in accordance with the terms of the OncoTrack Project Agreement and to the extent in compliance with the respective informed consent obtained. 8 Publications 5The RECIPIENT agrees to acknowledge in any RECIPIENT’s work based in whole or part on the DATA and/or SAMPLES, any PROVIDER publications which encompass and from which DATA and/or SAMPLES derive, the respective version of the DATA and/or SAMPLES 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 and/or SAMPLES 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 and/or SAMPLES by the RECIPIENT. The right to publish pursuant to this Section 8 is subject to Section 3 above (Confidentiality) and the informed consents of the DATA SUBJECTS. 9 Termination of Agreement and Consequences 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 alteration to the provisions of this Agreement, in which case the RECIPIENT may accept such alterations or a termination of this Agreement. Either party shall have the right to terminate this Agreement with three (3) weeks’ prior 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 and/or SAMPLES 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 and/or SAMPLES. Sections 3, 4, 8, 9 and 12 of this Agreement and all other obligations under this Agreement, which by their very nature are intended to survive such termination or expiration remain in full force and effect in case of an expiration or termination of this Agreement. 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 (i) stipulated in this Agreement or (ii) that 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. 10 Costs The RECIPIENT acknowledges that PROVIDER shall incur costs in providing the DATA and/or SAMPLES to the RECIPIENT, including but not limited to administrative costs and the cost of obtaining appropriate data storage devices. The RECIPIENT agrees to pay, at the request of PROVIDER, such reasonable costs as PROVIDER 6may incur in providing the DATA and/or SAMPLES, within thirty (30) days after having received an invoice by PROVIDER consistent with the current provisions of the applicable laws and regulations (e.g., German VAT Act (Umsatzsteuergesetz - UStG) as amended from time to time. 11 Limitation of Liability The RECIPIENT acknowledges that PROVIDER and all other parties involved in the creation, funding or protection of the DATA and/or SAMPLES: a) Make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of the DATA and/or SAMPLES; and b) Except to the extent prohibited by law, the RECIPIENT assumes all liability which may arise from its use, storage or disposal of the DATA and/or SAMPLES. PROVIDER will not be liable to the RECIPIENT for any loss, claim or demand made by the RECIPIENT, or made against the RECIPIENT by any other party, due to or arising from the use of the DATA and/or SAMPLES by the RECIPIENT, except to the extent permitted by mandatory statutory law or when caused by the gross negligence or wilful misconduct of PROVIDER. The RECIPIENT understands that all the DATA and/or SAMPLES are protected by INTELLECTUAL PROPERTY rights, such that duplication or sale of all of or part of the DATA and/or SAMPLES on any media is not permitted under any circumstances, except with the prior written consent of PROVIDER. In no event shall PROVIDER be liable for any use by RECIPIENT of the PROVIDER DATA and/or SAMPLES or any loss, claim, damage or liability, of whatsoever kind of nature, which may arise from or in connection with this Agreement or the use, handling or storage of the PROVIDER DATA and/or SAMPLES or derived from PROVIDER DATA by the RECIPIENT. 12 Governing Law This Agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this Agreement or its formation) shall be construed, interpreted and governed by the laws of Germany excluding its conflict of law rules and the United Nations Convention on Contracts for the International Sales of Goods (CISG) and shall be subject to the exclusive jurisdiction of the competent courts in Berlin. 13 Miscellaneous Notices: Any notice required or permitted to be given under this Agreement shall be in writing, unless otherwise set forth in this Agreement. Notice shall be deemed effective for all purposes upon the earliest of (i) the date of actual receipt, or (ii) if mailed or couriered the date of delivery set forth in the respective return receipt. Entire Agreement: This Agreement and its Annexes set forth the entire understanding and agreement of the PARTIES relating to the subject matter hereof. Amendment: No amendment, modification or addition to this Agreement and its Annexes shall be effective or binding on either PARTY unless set forth in writing and 7signed by both PARTIES. The same shall apply to a waiver of this written form requirement. Assignment: Unless otherwise set forth in this Agreement, no PARTY may assign any rights or delegate any duties or obligations under this Agreement without the prior written consent of the other, except that PROVIDER may assign this Agreement to any of its AFFILIATES without the consent of RECIPIENT. Independent Contractor: Each PARTY to this Agreement shall act as an independent contractor and nothing in this Agreement shall be construed to create a partnership, joint venture or agency relationship between the PARTIES. Severability: The invalidity or unenforceability of a particular provision of this Agreement shall not affect the validity or enforceability of the remaining provisions. The PARTIES shall replace the invalid or unenforceable provision with a valid and enforceable provision that comes closest to effectuating the intent of the PARTIES at the time of the Agreement's execution. The same shall apply if the Agreement is partially incomplete. 8AGREED by the PARTIES through their authorised signatories PROVIDER: Authorised Signature: Name: Title: Date: Authorised Signature: Name: Title: Date: RECIPIENT: Authorised Signature: Name: Title: Date: RECIPIENT SCIENTIST: The RECIPIENT SCIENTIST acknowledges the contents of this Agreement and agrees to comply with the obligations herein. For the avoidance of doubt the RECIPIENT SCIENTIST is not a party to this Agreement. (see Annex 1 for further reading and information) Signature: Name: Title: Date: Email: 9Annex 1 to Data and Samples Transfer Agreement for Research Purposes IT Security Access to DATA and/or SAMPLES covered by this DATA and SAMPLES Transfer Agreement is a procedure that entails legal and ethical obligations. We require that you and your institution has adequate information technology (IT) policies in place that meet industry standards and include, in particular, the following items: Should personal data be automatically processed or used, this shall be organised within the agency or company to ensure that it meets data protection requirements. Depending on the type of personal data or data categories to be protected, the measures taken shall, 1. Deny unauthorized access to data processing facilities in which personal data is processed or used (physical access controls), 2. Prevent unauthorised persons from using data processing systems (access controls), 3. Ensure that authorised users only have access to the DATA and/or SAMPLES to which they have access rights, and that personal data cannot be read, copied, modified or deleted by unauthorised persons during processing or use, and after storage (user-access control), 4. Ensure that personal data cannot be read, copied, modified or deleted by unauthorised persons during electronic transmission or during their transport or their storage on data carriers, and that it can be verified and established at which points a transmission of personal data by data transmission equipment (transmission control) is foreseen, 5. Ensure that it can be subsequently verified and established whether and by whom personal data are entered, modified or deleted in the data processing systems (input control), 6. Ensure that personal data which are processed on behalf of clients can be processed only in accordance with the instructions of the client (job control), 7. Ensure that personal data are protected against accidental destruction or loss (availability control), 8. Ensure that DATA and/or SAMPLES collected for different purposes can be processed separately. One measure, in particular, to be taken in compliance with paragraph 2, numbers 2-4, is the use of state-of-the-art encryption methods. In the event that the Recipient becomes aware that there has been a breach or suspected breach of the agreement, the Recipient shall immediately notify PROVIDER by telephone followed by written notice. RECIPIENT SCIENTIST: Signature: Name: Title: Date: Email: 10Annex 2 to Data and Samples Transfer Agreement for Research Purposes Data 11Annex 3 to Data Transfer Agreement of Human Data for Research Purposes Purpose of the Project 12Please send completed signature pages to: PROVIDER [INSERT: Contact information for PROVIDER]

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
EGAS00001001752 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
EGAF00001166648 fastq.gz 1.0 GB
EGAF00001166649 fastq.gz 1.0 GB
EGAF00001166650 fastq.gz 1.0 GB
EGAF00001166651 fastq.gz 1.0 GB
EGAF00001166652 fastq.gz 1.0 GB
EGAF00001166653 fastq.gz 1.0 GB
EGAF00001166654 fastq.gz 1.0 GB
EGAF00001166655 fastq.gz 1.0 GB
EGAF00001166998 fastq.gz 1.7 GB
EGAF00001166999 fastq.gz 1.7 GB
EGAF00001167000 fastq.gz 1.7 GB
EGAF00001167001 fastq.gz 1.7 GB
EGAF00001167002 fastq.gz 1.7 GB
EGAF00001167003 fastq.gz 1.7 GB
EGAF00001167004 fastq.gz 1.7 GB
EGAF00001167005 fastq.gz 1.7 GB
EGAF00001167518 fastq.gz 1.3 GB
EGAF00001167519 fastq.gz 1.3 GB
EGAF00001167520 fastq.gz 1.3 GB
EGAF00001167521 fastq.gz 1.3 GB
EGAF00001167522 fastq.gz 1.3 GB
EGAF00001167523 fastq.gz 1.3 GB
EGAF00001167524 fastq.gz 1.3 GB
EGAF00001167525 fastq.gz 1.3 GB
EGAF00001167783 fastq.gz 897.8 MB
EGAF00001167784 fastq.gz 911.6 MB
EGAF00001167785 fastq.gz 890.9 MB
EGAF00001167786 fastq.gz 903.6 MB
EGAF00001167787 fastq.gz 894.4 MB
EGAF00001167788 fastq.gz 906.1 MB
EGAF00001167789 fastq.gz 887.8 MB
EGAF00001167790 fastq.gz 900.5 MB
EGAF00001168103 fastq.gz 1.5 GB
EGAF00001168104 fastq.gz 1.5 GB
EGAF00001168105 fastq.gz 1.5 GB
EGAF00001168106 fastq.gz 1.5 GB
EGAF00001168107 fastq.gz 1.5 GB
EGAF00001168108 fastq.gz 1.5 GB
EGAF00001168109 fastq.gz 1.5 GB
EGAF00001168110 fastq.gz 1.5 GB
40 Files (51.5 GB)