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Spatial RNA-sequencing of metastatic melanoma

We performed RNA sequencing of 48 different regions sub-sampled from a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor. RNAseq was performed on samples with a minimum RNA integrity number (RIN) of 5.5 except for two cases (6A10 and 8A3) with RINs greater than 3. A minimum of 700ng of RNA were required for all samples undergoing RNAseq. Paired-end transcriptome reads were aligned using TopHat2, to the UCSC hg19 reference genome.

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The University of Texas MD Anderson Cancer Center Genomic Medicine Data Access Committee

DATA ACCESS AGREEMENT This Data Access Agreement (“Agreement”), effective as of the ____ day of _________________, 20__ (“Effective Date”), is by and between The University of Texas M. D. Anderson Cancer Center, an institution of The University of Texas System and an agency of the State of Texas, with an address at 1515 Holcombe Boulevard, Houston, Texas 77030 (“Provider”), and ________________________________ (“Recipient”) on behalf of its investigator _______ (“Recipient Investigator”) (collectively, the “Parties”; each, a “Party”). RECITALS Provider maintains the following de-identified data in the European Genome-phenome Archive (EGA) managed by the European Bioinformatics Institute ________________ (“Data”), and Provider is willing to allow Recipient to access such Data from the EGA for the internal noncommercial research purposes of _______________ (“Purpose”), pursuant to the terms of this Agreement. In consideration of the mutual promises and covenants herein, and for other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, the Parties agree as follows: 1. The Data will be used solely for the Research by Recipient Investigator at Recipient, and may not be transferred to any other investigator or to any third party without prior written permission from Provider. The Material may not be used for any purpose other than the Research, including without limitation for any commercial purpose or for research in human subjects (including, without limitation, in diagnostic testing). 2. Neither Recipient nor Recipient Investigator shall disclose Data to any person or party other than the Recipient Investigator hereunder without Provider’s prior written consent. 3. The Data will be used in compliance with all applicable laws, regulations, and guidelines applicable to the Data, including without limitation any applicable export controls. 4. In any publication resulting from use of the Data, Recipient and Recipient Investigator shall acknowledge Department of Genomic Medicine (“Provider Investigator”) and Provider as the provider of the Data. 5. This Agreement shall be effective as of the Effective Date and shall remain effective until completion of the Research. Either Party may terminate this Agreement with or without cause upon thirty (30) days’ written notice to the other Party. Upon expiration or termination of this Agreement for any reason, Recipient shall destroy all Data received pursuant to this Agreement. 6. Any notice permitted or required as provided for herein shall be in writing and to the contact and address as noted below or as may be provided by either party to the other in writing from time to time. Notice to Provider shall be to: Chief Legal Officer The University of Texas M. D. Anderson Cancer Center 7007 Bertner Ave., 1MC11.3433, Suite 1674 Houston, Texas 77030 Phone: 713-745-6633; Facsimile: 713-745-6029 With a copy to: The University of Texas M. D. Anderson Cancer Center 2 1515 Holcombe Blvd., FCT 8.5025 Office of Research Administration Attn: Executive Director, Research Administration Houston, TX 77030 Phone: 713-792-3672; Facsimile: 713-792-7455 Notice to Recipient shall be to: [insert] 7. In the event Protected Health Information (“PHI”), as defined by the federal Health Insurance Portability and Accountability Act of 1996 (“HIPAA”), as amended, is inadvertently created, accessed by, and/or disclosed to Recipient in connection with this Agreement, Recipient will immediately notify the Provider and will return to Provider or destroy such PHI, in accordance with the Provider’s instructions. Pending return or destruction of any PHI, Recipient shall maintain the confidentiality of all Data (including the PHI) and use appropriate safeguards to prevent access to, use, or disclosure of Data (including the PHI). 8. PROVIDER MAKES NO REPRESENTATION OR WARRANTY CONCERNING THE MATERIAL, INCLUDING WITHOUT LIMITATION, WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. 9. Recipient Investigator and Recipient accept all liability for any use of the Data and for any loss, claim, or damage which may arise from or in connection with this Agreement or the use, handling or storage of the Data and in no event shall Provider or Provider Investigator be liable for any such use, loss, claim or damage. [Insert Recipient Name Here] THE UNIVERSITY OF TEXAS M. D. ANDERSON CANCER CENTER By: By: Name: Name: Title: Title: Date: Date: Read and Understood: Recipient Scientist: Provider Scientist: [Insert Name and Title Here] [Insert Name and Title Here] Date: 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
EGAS00001003292 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
EGAF00003292764 bam 7.4 GB
EGAF00003292765 bam 7.6 GB
EGAF00003292766 bam 8.4 GB
EGAF00003292767 bam 9.4 GB
EGAF00003292768 bam 9.2 GB
EGAF00003292769 bam 6.8 GB
EGAF00003292770 bam 9.3 GB
EGAF00003292771 bam 9.3 GB
EGAF00003292772 bam 8.6 GB
EGAF00003292773 bam 10.8 GB
EGAF00003292774 bam 8.6 GB
EGAF00003292775 bam 7.9 GB
EGAF00003292776 bam 7.9 GB
EGAF00003292777 bam 7.4 GB
EGAF00003292778 bam 8.0 GB
EGAF00003292779 bam 9.4 GB
EGAF00003292780 bam 10.0 GB
EGAF00003292781 bam 7.5 GB
EGAF00003292782 bam 7.4 GB
EGAF00003292783 bam 7.5 GB
EGAF00003292784 bam 10.2 GB
EGAF00003292785 bam 8.3 GB
EGAF00003292786 bam 7.6 GB
EGAF00003292787 bam 9.0 GB
EGAF00003292788 bam 7.8 GB
EGAF00003292789 bam 9.0 GB
EGAF00003292790 bam 9.7 GB
EGAF00003292791 bam 7.7 GB
EGAF00003292792 bam 7.3 GB
EGAF00003292793 bam 11.0 GB
EGAF00003292794 bam 9.7 GB
EGAF00003292795 bam 10.8 GB
EGAF00003292796 bam 11.5 GB
EGAF00003292797 bam 10.6 GB
EGAF00003292798 bam 9.7 GB
EGAF00003292799 bam 9.5 GB
EGAF00003292800 bam 9.4 GB
EGAF00003292801 bam 9.9 GB
EGAF00003292802 bam 9.8 GB
EGAF00003292803 bam 10.2 GB
EGAF00003292804 bam 10.1 GB
EGAF00003292805 bam 8.8 GB
EGAF00003292806 bam 10.5 GB
EGAF00003292807 bam 9.1 GB
EGAF00003292808 bam 9.3 GB
EGAF00003292809 bam 9.9 GB
EGAF00003292810 bam 10.5 GB
EGAF00003292811 bam 11.5 GB
48 Files (436.9 GB)